García Gil, María Rosario - Forest Tree Genetics and Breeding

@article{ortiz_genomic_2024,
	title = {Genomic {Prediction} for {Inbred} and {Hybrid} {Polysomic} {Tetraploid} {Potato} {Offspring}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2077-0472},
	url = {https://www.mdpi.com/2077-0472/14/3/455},
	doi = {10.3390/agriculture14030455},
	abstract = {Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.},
	language = {en},
	number = {3},
	urldate = {2024-04-04},
	journal = {Agriculture},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = mar,
	year = {2024},
	note = {Number: 3
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Solanum tuberosum}, Nordic latitude, crossing, genomic estimated breeding values, linear models, polyploidy, selfing, tetrasomic inheritance},
	pages = {455},
}

Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.

@article{hayatgheibi_implications_2024,
	title = {Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in {Norway} spruce},
	volume = {25},
	issn = {2730-6844},
	url = {https://doi.org/10.1186/s12863-024-01241-x},
	doi = {10.1186/s12863-024-01241-x},
	abstract = {Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).},
	number = {1},
	urldate = {2024-07-01},
	journal = {BMC Genomic Data},
	author = {Hayatgheibi, Haleh and Hallingbäck, Henrik R. and Lundqvist, Sven-Olof and Grahn, Thomas and Scheepers, Gerhard and Nordström, Peter and Chen, Zhi-Qiang and Kärkkäinen, Katri and Wu, Harry X. and García-Gil, M. Rosario},
	month = jun,
	year = {2024},
	keywords = {Cross-validation, Norway spruce, Population structure, Prediction accuracy, Wood properties},
	pages = {60},
}

Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).

@article{ranade_lignin_2024,
	title = {Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2767-3812},
	shorttitle = {Lignin biosynthesis pathway repressors in gymnosperms},
	url = {https://www.maxapress.com/article/doi/10.48130/forres-0024-0029},
	doi = {10.48130/forres-0024-0029},
	abstract = {{\textless}p{\textgreater}Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from \textit{Ginkgo} was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-09-27},
	journal = {Forestry Research},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = sep,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: forres-0024-0029
Primary\_atype: Forestry Research
Publisher: Maximum Academic Press
Subject\_term: MINI REVIEW
Subject\_term\_id: MINI REVIEW},
}

\textlessp\textgreaterLignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.\textless/p\textgreater

@article{lecoy_analysis_2023,
	title = {Analysis of the {ASR} and {LP3} homologous gene families reveal positive selection acting on {LP3}-3 gene},
	volume = {850},
	issn = {0378-1119},
	url = {https://www.sciencedirect.com/science/article/pii/S0378111922007557},
	doi = {10.1016/j.gene.2022.146935},
	abstract = {Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Gene},
	author = {Lecoy, Jonathan and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jan,
	year = {2023},
	keywords = {ABA/WDS, Codon usage, Drought resistance, GC-content, Selective pressure},
	pages = {146935},
}

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.

@article{ranade_clinal_2023,
	title = {Clinal variation in {PHY} ({PAS} domain) and {CRY} ({CCT} domain)—{Signs} of local adaptation to light quality in {Norway} spruce},
	volume = {n/a},
	copyright = {© 2023 The Authors. Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14638},
	doi = {10.1111/pce.14638},
	abstract = {Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.},
	language = {en},
	number = {n/a},
	urldate = {2023-06-09},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14638},
	keywords = {SNP, cline, cryptochrome, missense mutation, photoreceptor, phytochrome, polymorphism},
}

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.

@article{tiret_divergent_2023,
	title = {Divergent selection predating the {Last} {Glacial} {Maximum} mainly acted on macro-phenotypes in {Norway} spruce},
	volume = {16},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13519},
	doi = {10.1111/eva.13519},
	abstract = {The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.},
	language = {en},
	number = {1},
	urldate = {2023-01-20},
	journal = {Evolutionary Applications},
	author = {Tiret, Mathieu and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Milesi, Pascal and Lascoux, Martin and Lundqvist, Sven-Olof and García-Gil, Maria Rosario},
	year = {2023},
	keywords = {Norway spruce, QST vs. FST, population structure, wood quality},
	pages = {163--172},
}

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

@article{ortiz_inbreeding_2023,
	title = {Inbreeding {Effects} on the {Performance} and {Genomic} {Prediction} for {Polysomic} {Tetraploid} {Potato} {Offspring} {Grown} at {High} {Nordic} {Latitudes}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4425},
	url = {https://www.mdpi.com/2073-4425/14/6/1302},
	doi = {10.3390/genes14061302},
	abstract = {Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p {\textless} 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p {\textless} 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19\%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.},
	language = {en},
	number = {6},
	urldate = {2023-06-30},
	journal = {Genes},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = jun,
	year = {2023},
	note = {Number: 6
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Solanum tuberosum} L., Fennoscandia, GEBV, QTL, Scandinavia, accuracy, genetic gains, germplasm enhancement, hybrid, inbred},
	pages = {1302},
}

Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p \textless 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p \textless 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.

@article{gil-munoz_qtl_2023,
	title = {{QTL} mapping of the narrow-branch “{Pendula}” phenotype in {Norway} spruce ({Picea} abies {L}. {Karst}.)},
	volume = {19},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-023-01599-6},
	doi = {10.1007/s11295-023-01599-6},
	abstract = {Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25\% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.},
	language = {en},
	number = {3},
	urldate = {2023-05-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gil-Muñoz, Francisco and Bernhardsson, Carolina and Ranade, Sonali Sachin and Scofield, Douglas G. and Pulkkinen, Pertti O. and Ingvarsson, Pär K. and García-Gil, M. Rosario},
	month = may,
	year = {2023},
	keywords = {Forest breeding, Genetic map, Pendula, Picea, QTL, Spruce},
	pages = {28},
}

Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.

@article{ranade_adaptive_2022,
	title = {Adaptive strategies of {Scots} pine under shade: increase in lignin synthesis and ecotypic variation in defence-related gene expression},
	volume = {2022-10},
	issn = {1399-3054},
	shorttitle = {Adaptive strategies of {Scots} pine under shade},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13792},
	doi = {10.1111/ppl.13792},
	abstract = {Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	month = sep,
	year = {2022},
	pages = {e13792},
}

Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.

@article{ranade_enhanced_2022,
	title = {Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in {Norway} spruce},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14387},
	doi = {10.1111/pce.14387},
	abstract = {During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.},
	language = {en},
	number = {9},
	urldate = {2022-08-19},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14387},
	keywords = {Conifer, Defense, Ecotypic variation, Immunity, Light quality, Lignin, Local adaptation, Norway spruce, R:FR ratio, RNA sequencing, Response to shade, conifer, disease resistance, far-red light, immunity, latitudinal cline, light quality, local adaptation, red light},
	pages = {2671--2681},
}

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

@article{chen_genetic_2022,
	title = {Genetic architecture behind developmental and seasonal control of tree growth and wood properties in {Norway} spruce},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.927673},
	abstract = {Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover {\textasciitilde}130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.},
	urldate = {2022-09-01},
	journal = {Frontiers in Plant Science},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Zhou, Linghua and Karlsson, Bo and Tuominen, Hannele and García-Gil, Maria Rosario and Wu, Harry X.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

@incollection{calleja-rodriguez_genomic_2022,
	address = {Cham},
	title = {Genomic {Selection} in {Scots} ({Pinus} {Sylvestris}) and {Radiata} ({Pinus} {Radiata}) {Pines}},
	isbn = {978-3-030-93390-6},
	url = {https://doi.org/10.1007/978-3-030-93390-6_11},
	abstract = {Pines are economically important species widely planted across the globe. Therefore, the industry is interested in increasing the efficacy of their breeding programs, which explains the urge to implement new technological solutions to increase breeding efficiency for traditional and novel breeding objectives. Recently, the development of genotyping platforms accessible even for non-model organisms such as Scots and radiata pines has made it possible to evaluate genomic selection for their breeding programs. Genomic studies in both species are limited by the size and complexity of their genomes; therefore, genotyping platforms based on reduced genome representation have been implemented. Genomic selection studies performed within their breeding programs show viability and potential to increase the intensity of genetic progress compared to conventional (i.e., pedigree-based) strategies. Additionally, genomic prediction of traits with challenging or costly phenotyping, such as forest diseases or wood quality and cell wall chemistry, might allow for large-scale screening and selection of individuals with superior traits. This chapter presents a review of the recent research on genomic selection for Scots pine in Sweden, and radiata pine in New Zealand, as well as future perspectives for the implementation of this methodology in their breeding programs.},
	language = {en},
	urldate = {2024-10-16},
	booktitle = {The {Pine} {Genomes}},
	publisher = {Springer International Publishing},
	author = {Calleja-Rodríguez, Ainhoa and Klápště, Jaroslav and Dungey, Heidi and Graham, Natalie and Ismael, Ahmed and García-Gil, Maria Rosario and Abrahamsson, Sara and Suontama, Mari},
	editor = {De La Torre, Amanda R.},
	year = {2022},
	doi = {10.1007/978-3-030-93390-6_11},
	pages = {233--250},
}

Pines are economically important species widely planted across the globe. Therefore, the industry is interested in increasing the efficacy of their breeding programs, which explains the urge to implement new technological solutions to increase breeding efficiency for traditional and novel breeding objectives. Recently, the development of genotyping platforms accessible even for non-model organisms such as Scots and radiata pines has made it possible to evaluate genomic selection for their breeding programs. Genomic studies in both species are limited by the size and complexity of their genomes; therefore, genotyping platforms based on reduced genome representation have been implemented. Genomic selection studies performed within their breeding programs show viability and potential to increase the intensity of genetic progress compared to conventional (i.e., pedigree-based) strategies. Additionally, genomic prediction of traits with challenging or costly phenotyping, such as forest diseases or wood quality and cell wall chemistry, might allow for large-scale screening and selection of individuals with superior traits. This chapter presents a review of the recent research on genomic selection for Scots pine in Sweden, and radiata pine in New Zealand, as well as future perspectives for the implementation of this methodology in their breeding programs.

@article{gauchan_annulohypoxylon_2021,
	title = {Annulohypoxylon sp. strain {MUS1}, an endophytic fungus isolated from {Taxus} wallichiana {Zucc}., produces taxol and other bioactive metabolites},
	volume = {11},
	issn = {2190-572X, 2190-5738},
	url = {http://link.springer.com/10.1007/s13205-021-02693-z},
	doi = {10/gkcr8j},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {3 Biotech},
	author = {Gauchan, Dhurva Prasad and Vélëz, Heriberto and Acharya, Ashesh and Östman, Johnny R. and Lundén, Karl and Elfstrand, Malin and García-Gil, M. Rosario},
	month = mar,
	year = {2021},
	pages = {152},
}

@article{chen_leveraging_2021,
	title = {Leveraging breeding programs and genomic data in {Norway} spruce ({Picea} abies {L}. {Karst}) for {GWAS} analysis},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02392-1},
	doi = {10.1186/s13059-021-02392-1},
	abstract = {Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genome Biology},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Li, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and García-Gil, Maria Rosario and Lascoux, Martin and Wu, Harry X.},
	month = jun,
	year = {2021},
	keywords = {Budburst stage, Frost damage, Genome-wide association study, MAP3K gene, Norway spruce, Wood quality},
	pages = {179},
}

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

@article{ahlinder_life_2021,
	title = {Life stage-specific inbreeding depression in long-lived {Pinaceae} species depends on population connectivity},
	volume = {11},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-021-88128-4},
	doi = {10.1038/s41598-021-88128-4},
	abstract = {Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Scientific Reports},
	author = {Ahlinder, Jon and Giles, Barbara E. and García-Gil, M. Rosario},
	month = apr,
	year = {2021},
	pages = {8834},
}

Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.

@article{ranade_molecular_2021,
	title = {Molecular signatures of local adaptation to light in {Norway} spruce},
	volume = {253},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-020-03517-9},
	doi = {10/gjd69n},
	abstract = {Abstract
            
              Main conclusion
              Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light.
            
            
              Abstract
              The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = feb,
	year = {2021},
	pages = {53},
}

Abstract Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

@article{zhou_effect_2020,
	title = {Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of {Norway} spruce},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6737-3},
	doi = {10.1186/s12864-020-6737-3},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (
                Picea abies
                (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments.
              
            
            
              Results
              GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30\% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95\% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12.
            
            
              Conclusions
              This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90\% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Zhou, Linghua and Chen, Zhiqiang and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {323},
}

Abstract Background Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. Results GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12. Conclusions This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

@article{gauchan_evaluation_2020,
	title = {Evaluation of antimicrobial, antioxidant and cytotoxic properties of bioactive compounds produced from endophytic fungi of {Himalayan} yew ({Taxus} wallichiana) in {Nepal}},
	volume = {9},
	issn = {2046-1402},
	url = {https://f1000research.com/articles/9-379/v2},
	doi = {10.12688/f1000research.23250.2},
	abstract = {Background:
              Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study,
              Taxus wallichiana,
              which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties.
            
            
              Methods:
              The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts.
            
            
              Results:
              Out of 16 different
              Taxus
              trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera:
              Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella
              and
              Daldinia
              . The ethyl acetate extracts isolated from three endophytic fungi:
              Alternaria alternata
              ,
              Cladosporium cladosporioides
              and
              Alternaria brassicae
              showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC
              50
              concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of
              C. cladosporioides
              and
              A. brassicae
              also showed promising antimicrobial activity against
              Escherichia coli
              ,
              Staphylococcus aureus
              and
              Bacillus subtilis
              with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC
              50
              of 104.2 and 125.9µg/ml, respectively.
            
            
              Conclusions:
              The crude fungal extracts obtained from endophytes:
              A. alternata
              ,
              C. cladosporioides
              and
              A. brassicae
              upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.},
	language = {en},
	urldate = {2021-06-07},
	journal = {F1000Research},
	author = {Gauchan, Dhurva Prasad and Kandel, Pratistha and Tuladhar, Astha and Acharya, Ashesh and Kadel, Upendra and Baral, Aayush and Shahi, Arjan Bir and García-Gil, María Rosario},
	month = oct,
	year = {2020},
	pages = {379},
}

Background: Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study, Taxus wallichiana, which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties. Methods: The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts. Results: Out of 16 different Taxus trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera: Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella and Daldinia . The ethyl acetate extracts isolated from three endophytic fungi: Alternaria alternata , Cladosporium cladosporioides and Alternaria brassicae showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC 50 concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of C. cladosporioides and A. brassicae also showed promising antimicrobial activity against Escherichia coli , Staphylococcus aureus and Bacillus subtilis with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC 50 of 104.2 and 125.9µg/ml, respectively. Conclusions: The crude fungal extracts obtained from endophytes: A. alternata , C. cladosporioides and A. brassicae upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.

@article{baison_genetic_2020,
	title = {Genetic control of tracheid properties in {Norway} spruce wood},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-72586-3},
	doi = {10.1038/s41598-020-72586-3},
	abstract = {Abstract
            
              Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (
              Picea abies
              (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are:
              Picea abies BIG GRAIN 2
              (
              PabBG2)
              with a predicted function in auxin transport and sensitivity, and
              MA\_373300g0010
              encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Baison, J. and Zhou, Linghua and Forsberg, Nils and Mörling, Tommy and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry X. and Mellerowicz, Ewa J. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {18089},
}

Abstract Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce ( Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 ( PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

@article{gil-munoz_transcriptomic_2020,
	title = {Transcriptomic {Analysis} {Reveals} {Salt} {Tolerance} {Mechanisms} {Present} in {Date}-{Plum} {Persimmon} {Rootstock} ({Diospyros} lotus {L}.)},
	volume = {10},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/10/11/1703},
	doi = {10/gjd6kb},
	abstract = {Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Agronomy},
	author = {Gil-Muñoz, Francisco and Delhomme, Nicolas and Quiñones, Ana and Naval, Maria del Mar and Badenes, Maria Luisa and García-Gil, M. Rosario},
	month = nov,
	year = {2020},
	pages = {1703},
}

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt–tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

@article{bernhardsson_ultra-dense_2019,
	title = {An {Ultra}-{Dense} {Haploid} {Genetic} {Map} for {Evaluating} the {Highly} {Fragmented} {Genome} {Assembly} of {Norway} {Spruce} ({Picea} abies )},
	volume = {9},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/9/5/1623/6026441},
	doi = {10/gjcr63},
	abstract = {Abstract
            Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60\% of the total genome size but is highly fragmented, consisting of \>10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6\% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8\% of the anchored scaffolds and 1.6\% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Bernhardsson, Carolina and Vidalis, Amaryllis and Wang, Xi and Scofield, Douglas G and Schiffthaler, Bastian and Baison, John and Street, Nathaniel R and García-Gil, M Rosario and Ingvarsson, Pär K},
	month = may,
	year = {2019},
	pages = {1623--1632},
}

Abstract Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

@article{calleja-rodriguez_analysis_2019,
	title = {Analysis of phenotypic- and {Estimated} {Breeding} {Values} ({EBV}) to dissect the genetic architecture of complex traits in a {Scots} pine three-generation pedigree design},
	volume = {462},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002251931830554X},
	doi = {10.1016/j.jtbi.2018.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Journal of Theoretical Biology},
	author = {Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik R. and Sillanpää, Mikko J. and Wu, Harry X. and Abrahamsson, Sara and García-Gil, Maria Rosario},
	month = feb,
	year = {2019},
	pages = {283--292},
}

@article{zhou_genetic_2019,
	title = {Genetic analysis of wood quality traits in {Norway} spruce open-pollinated progenies and their parent plus trees at clonal archives and the evaluation of phenotypic selection of plus trees},
	volume = {49},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0117},
	doi = {10/gjcjw5},
	abstract = {A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h
              2
              ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h
              2
              estimate, selection of the best clones from clonal archives would be an effective alternative.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Zhou, Linghua and Chen, Zhiqiang and Lundqvist, Sven-Olof and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {810--818},
}

A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h 2 ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h 2 estimate, selection of the best clones from clonal archives would be an effective alternative.

@article{baison_genomewide_2019,
	title = {Genome‐wide association study identified novel candidate loci affecting wood formation in {Norway} spruce},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14429},
	doi = {10/gjcj3d},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Baison, John and Vidalis, Amaryllis and Zhou, Linghua and Chen, Zhi‐Qiang and Li, Zitong and Sillanpää, Mikko J. and Bernhardsson, Carolina and Scofield, Douglas and Forsberg, Nils and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry and Ingvarsson, Pär K. and Lundqvist, Sven‐Olof and Niittylä, Totte and García‐Gil, M Rosario},
	month = oct,
	year = {2019},
	pages = {83--100},
}

@article{ranade_global_2019,
	title = {Global gene expression analysis in etiolated and de-etiolated seedlings in conifers},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0219272},
	doi = {10/gjcsvr},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, M. Rosario},
	editor = {Zhang, Jin-Song},
	month = jul,
	year = {2019},
	pages = {e0219272},
}

@article{ranade_transcriptome_2019,
	title = {Transcriptome analysis of shade avoidance and shade tolerance in conifers},
	volume = {250},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-019-03160-z},
	doi = {10/gjcr99},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {299--318},
}

@article{chen_accuracy_2018,
	title = {Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in {Norway} spruce},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5256-y},
	doi = {10/ghk9pc},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Karlsson, Bo and Andersson, Bengt and Westin, Johan and García-Gil, María Rosario and Wu, Harry X.},
	month = dec,
	year = {2018},
	pages = {946},
}

@article{lundqvist_age_2018,
	title = {Age and weather effects on between and within ring variations of number, width and coarseness of tracheids and radial growth of young {Norway} spruce},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1136-x},
	doi = {10.1007/s10342-018-1136-x},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Lundqvist, Sven-Olof and Seifert, Stefan and Grahn, Thomas and Olsson, Lars and García-Gil, Maria Rosario and Karlsson, Bo and Seifert, Thomas},
	month = oct,
	year = {2018},
	pages = {719--743},
}

@article{hayatgheibi_genetic_2018,
	title = {Genetic control of transition from juvenile to mature wood with respect to microfibril angle in {Norway} spruce ( \textit{{Picea} abies} ) and lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0140},
	doi = {10.1139/cjfr-2018-0140},
	abstract = {Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
              2
              ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
              2
              were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Forsberg, Nils Erik Gustaf and Lundqvist, Sven-Olof and Mörling, Tommy and Mellerowicz, Ewa J. and Karlsson, Bo and Wu, Harry X. and García-Gil, M. Rosario},
	month = nov,
	year = {2018},
	pages = {1358--1365},
}

Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h 2 ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h 2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.

@article{razzak_differential_2017,
	title = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light: {Scots} pine response to light intensity and shade},
	volume = {40},
	issn = {01407791},
	shorttitle = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light},
	url = {http://doi.wiley.com/10.1111/pce.12921},
	doi = {10.1111/pce.12921},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Razzak, Abdur and Ranade, Sonali Sachin and Strand, Åsa and García-Gil, M. R.},
	month = aug,
	year = {2017},
	pages = {1332--1340},
}

@article{ranade_application_2016,
	title = {Application of monochromatic blue light during germination and hypocotyl development improves outplanted {Scots} pine ({Pinus} sylvestris {L}.) trees performance},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S037811271500657X},
	doi = {10.1016/j.foreco.2015.11.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Ranade, Sonali Sachin and García Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {368--374},
}

@article{ranade_non-functional_2016,
	title = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch}): insights from in silico analysis of nuclear and organellar genomes},
	volume = {291},
	issn = {1617-4615, 1617-4623},
	shorttitle = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch})},
	url = {http://link.springer.com/10.1007/s00438-015-1159-7},
	doi = {10.1007/s00438-015-1159-7},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Molecular Genetics and Genomics},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Rosselló, Josep A.},
	month = apr,
	year = {2016},
	pages = {935--941},
}

@article{bernhardsson_present_2016,
	title = {Present genetic structure is congruent with the common origin of distant {Scots} pine populations in its {Romanian} distribution},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112715006052},
	doi = {10.1016/j.foreco.2015.10.047},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Bernhardsson, C. and Floran, V. and Ganea, S.L. and García-Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {131--143},
}

@article{ranade_fungal_2015,
	title = {Fungal {Infection} {Increases} the {Rate} of {Somatic} {Mutation} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {106},
	issn = {1465-7333 (Electronic) 0022-1503 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25890976},
	doi = {10.1093/jhered/esv017},
	abstract = {Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {J Hered},
	author = {Ranade, S. S. and Ganea, L. S. and Razzak, A. M. and Garcia Gil, M. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/04/22},
	keywords = {*Mutation Rate, Basidiomycota/*pathogenicity, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Genome, Plant, Genomic Instability, Genotype, Host-Pathogen Interactions/*genetics, Microsatellite Repeats, Mutation, Pinus sylvestris/*genetics/microbiology, Plant Diseases/genetics/*microbiology, Scots pine, Sequence Analysis, DNA, Somatic mutation., Sweden, abiotic stress, microsatellite, simple sequence repeats},
	pages = {386--94},
}

Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).

@article{li_functional_2014,
	title = {Functional {Multi}-{Locus} {QTL} {Mapping} of {Temporal} {Trends} in {Scots} {Pine} {Wood} {Traits}},
	volume = {4},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/4/12/2365/6025852},
	doi = {10/f3p5gx},
	abstract = {Abstract
            Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Li, Zitong and Hallingbäck, Henrik R and Abrahamsson, Sara and Fries, Anders and Gull, Bengt Andersson and Sillanpää, Mikko J and García-Gil, M Rosario},
	month = dec,
	year = {2014},
	pages = {2365--2379},
}

Abstract Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.

@article{abrahamsson_maternal_2013,
	title = {Maternal heterozygosity and progeny fitness association in an inbred {Scots} pine population},
	volume = {141},
	issn = {0016-6707, 1573-6857},
	url = {http://link.springer.com/10.1007/s10709-013-9704-y},
	doi = {10/f2242n},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Genetica},
	author = {Abrahamsson, S. and Ahlinder, J. and Waldmann, P. and García-Gil, M. R.},
	month = mar,
	year = {2013},
	pages = {41--50},
}

@article{ranade_pinus_2013,
	title = {Pinus taeda {cDNA} {Microarray} as a {Tool} for {Candidate} {Gene} {Identification} for {Local} {Red}/{Far}-{Red} {Light} {Adaptive} {Response} in {Pinus} sylvestris},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=28683},
	doi = {10/gjcmm4},
	abstract = {Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-21},
	journal = {American Journal of Plant Sciences},
	author = {Ranade, Sonali S. and Abrahamsson, Sara and Niemi, Juha and García-Gil, María Rosario},
	month = mar,
	year = {2013},
	note = {Number: 3
Publisher: Scientific Research Publishing},
	pages = {479--493},
}

Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{floran_organelle_2011,
	title = {Organelle {Genetic} {Diversity} and {Phylogeography} of {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {39},
	doi = {10/gg32mz},
	abstract = {The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Floran, Valentina and Sestras, Radu and Garcia Gil, Rosario},
	month = may,
	year = {2011},
	pages = {317--322},
}

The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.

@incollection{gonzalez-martinez_patterns_2011,
	title = {Patterns of {Nucleotide} {Diversity} and {Association} {Mapping}},
	isbn = {978-0-429-06593-4},
	abstract = {Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.},
	booktitle = {Genetics, {Genomics} and {Breeding} of {Conifers}},
	publisher = {CRC Press},
	author = {González-Martínez, S. C. and Dillon, S. and Garnier-Géré, P. H. and Krutovsky, K. V. and Alía, R. and Burgarella, C. and Eckert, A. J. and García-Gil, M. R. and Grivet, D. and Heuertz, M.},
	year = {2011},
	note = {Num Pages: 36},
}

Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.

@article{garcia-gil_evolutionary_2008,
	title = {Evolutionary {Aspects} of {Functional} and {Pseudogene} {Members} of the {Phytochrome} {Gene} {Family} in {Scots} {Pine}},
	volume = {67},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-008-9135-z},
	doi = {10/dmzkqj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Molecular Evolution},
	author = {García-Gil, Maria Rosario},
	month = aug,
	year = {2008},
	pages = {222--232},
}

@article{pyhajarvi_demographic_2007,
	title = {Demographic {History} {Has} {Influenced} {Nucleotide} {Diversity} in {European} \textit{{Pinus} sylvestris} {Populations}},
	volume = {177},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/177/3/1713/6064487},
	doi = {10/cmrqmt},
	abstract = {Abstract
            To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Pyhäjärvi, Tanja and García-Gil, M Rosario and Knürr, Timo and Mikkonen, Merja and Wachowiak, Witold and Savolainen, Outi},
	month = nov,
	year = {2007},
	pages = {1713--1724},
}

Abstract To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.

@article{notivol_genetic_2007,
	title = {Genetic variation of growth rhythm traits in the limits of a latitudinal cline in {Scots} pine},
	volume = {37},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X06-243},
	doi = {10/bjtx48},
	abstract = {Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q
              ST
              = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14\% ± 8\%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Notivol, E. and García-Gil, M. R. and Alía, R. and Savolainen, O.},
	month = mar,
	year = {2007},
	pages = {540--551},
}

Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q ST = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14% ± 8%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.

@article{waldmann_comparing_2005,
	title = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits: an application to {Pinus} sylvestris},
	volume = {94},
	copyright = {2005 The Genetics Society},
	issn = {1365-2540},
	shorttitle = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits},
	url = {https://www.nature.com/articles/6800672},
	doi = {10.1038/sj.hdy.6800672},
	abstract = {Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {Heredity},
	author = {Waldmann, P. and García-Gil, M. R. and Sillanpää, M. J.},
	month = jun,
	year = {2005},
	note = {Number: 6
Publisher: Nature Publishing Group},
	pages = {623--629},
}

Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

@article{savolainen_genetic_2004,
	title = {Genetic variation in cessation of growth and frost hardiness and consequences for adaptation of {Pinus} sylvestris to climatic changes},
	volume = {197},
	issn = {0378-1127},
	doi = {10/dvn6cp},
	abstract = {Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.},
	language = {English},
	number = {1-3},
	journal = {Forest Ecology and Management},
	author = {Savolainen, O. and Bokma, F. and Garcia-Gil, R. and Komulainen, P. and Repo, T.},
	month = aug,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000223382700007},
	keywords = {abies l karst, adaptation, boreal forests, climate change, cold-hardiness, contorta, f-st, frost hardiness, nucleotide diversity, pollen migration, populations, responses, scots pine, timing of growth, traits},
	pages = {79--89},
}

Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.

@article{komulainen_comparing_2003,
	title = {Comparing {EST}-based genetic maps between {Pinus} sylvestris and {Pinus} taeda},
	volume = {107},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-003-1312-2},
	doi = {10/fvc7mz},
	abstract = {A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40\% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Theoretical and Applied Genetics},
	author = {Komulainen, P. and Brown, G. R. and Mikkonen, M. and Karhu, A. and García-Gil, M. R. and O'Malley, D. and Lee, B. and Neale, D. B. and Savolainen, O.},
	month = aug,
	year = {2003},
	pages = {667--678},
}

A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.

@article{garcia-gil_nucleotide_2003,
	title = {Nucleotide diversity at two phytochrome loci along a latitudinal cline in {Pinus} sylvestris},
	volume = {12},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-294X.2003.01826.x},
	doi = {10.1046/j.1365-294X.2003.01826.x},
	abstract = {Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12–15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; π was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.},
	language = {en},
	number = {5},
	urldate = {2024-10-02},
	journal = {Molecular Ecology},
	author = {García-Gil, M. R. and Mikkonen, M. and Savolainen, O.},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-294X.2003.01826.x},
	keywords = {Pinus sylvestris, bud set date, latitudinal cline, nucleotide diversity, photoperiod, phytochrome},
	pages = {1195--1206},
}

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12–15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; π was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.