@article{han_easyomics_2025,
	title = {{EasyOmics}: {A} graphical interface for population-scale omics data association, integration, and visualization},
	volume = {6},
	issn = {2590-3462},
	shorttitle = {{EasyOmics}},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000550},
	doi = {10.1016/j.xplc.2025.101293},
	abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.},
	number = {5},
	urldate = {2026-05-19},
	journal = {Plant Communications},
	author = {Han, Yu and Du, Qiao and Dai, Yifei and Gu, Shaobo and Lei, Mengyu and Liu, Wei and Zhang, Wenjia and Zhu, Mingjia and Feng, Landi and Si, Huan and Liu, Jianquan and Zan, Yanjun},
	month = may,
	year = {2025},
	keywords = {association analysis, bioinformatics, data visualization, omics data},
	pages = {101293},
}

The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.

@article{wang_identification_2025,
	title = {Identification, {Characterization}, {Expression} {Profiling} and {Functional} {Analysis} of {Tobacco} {CalS} {Gene} {Family}},
	volume = {15},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/15/4/884},
	doi = {10.3390/agronomy15040884},
	abstract = {Callose plays an important role in plant development and in response to a wide range of biotic and abiotic stresses. However, the systematic identification of callose synthase (CalS), the major enzyme for callose biosynthesis, has been delayed in crops, especially in Solanaceae. In the current research, 18 CalS genes (NtCalS1–NtCalS18) were identified in Nicotiana tabacum and classified into four subfamilies. A comprehensive analysis of their physicochemical properties, gene structure, and evolutionary history highlighted their evolutionary conservation. We also identified a number of NtCalSs that responded to the infection with Phytophthora nicotianae and Ralstonia solanacearum, as well as to drought and cold treatments, by analyzing RNA-seq data. NtCalS1 and NtCalS12, a highly homologous gene pair, were selected to create mutants using the CRISPR-Cas9 technology for their drastic response to Phytophthora nicotianae infection as well as the strong expression levels in roots. The mutants with the simultaneous knockout of NtCalS1 and NtCalS12, compared with the control plants, displayed more resistance to tobacco black shank caused by Phytophthora nicotianae. Furthermore, the real-time quantitative PCR (qRT-PCR) assay showed that the knockout of NtCalS1 and NtCalS12 activated the signaling pathways mediated by plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) before and after the infection of Phytophthora nicotianae and thus may have contributed to tobacco immunity against black shank. These findings contribute valuable information for further understanding the roles of CalS genes in tobacco stress responses and provide alternative genes for resistance improvement.},
	language = {en},
	number = {4},
	urldate = {2026-05-19},
	journal = {Agronomy},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Wang, Hong and Meng, He and Qi, Xiaohan and Pan, Yi and Ji, Bailu and Wen, Liuying and Zan, Yanjun and Si, Huan and Wang, Yuanying and Liu, Dan and Yang, Aiguo and Liu, Zhengwen and Cheng, Lirui},
	month = apr,
	year = {2025},
	keywords = {\textit{CalS} gene family, \textit{Nicotiana tabacum}, callose synthase, expression analysis, gene editing, stress response},
	pages = {884},
}

Callose plays an important role in plant development and in response to a wide range of biotic and abiotic stresses. However, the systematic identification of callose synthase (CalS), the major enzyme for callose biosynthesis, has been delayed in crops, especially in Solanaceae. In the current research, 18 CalS genes (NtCalS1–NtCalS18) were identified in Nicotiana tabacum and classified into four subfamilies. A comprehensive analysis of their physicochemical properties, gene structure, and evolutionary history highlighted their evolutionary conservation. We also identified a number of NtCalSs that responded to the infection with Phytophthora nicotianae and Ralstonia solanacearum, as well as to drought and cold treatments, by analyzing RNA-seq data. NtCalS1 and NtCalS12, a highly homologous gene pair, were selected to create mutants using the CRISPR-Cas9 technology for their drastic response to Phytophthora nicotianae infection as well as the strong expression levels in roots. The mutants with the simultaneous knockout of NtCalS1 and NtCalS12, compared with the control plants, displayed more resistance to tobacco black shank caused by Phytophthora nicotianae. Furthermore, the real-time quantitative PCR (qRT-PCR) assay showed that the knockout of NtCalS1 and NtCalS12 activated the signaling pathways mediated by plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) before and after the infection of Phytophthora nicotianae and thus may have contributed to tobacco immunity against black shank. These findings contribute valuable information for further understanding the roles of CalS genes in tobacco stress responses and provide alternative genes for resistance improvement.

@article{si_development_2025,
	title = {Development of two sets of tobacco chromosome segment substitution lines and {QTL} mapping for agronomic and disease resistance traits},
	volume = {226},
	issn = {0926-6690},
	url = {https://www.sciencedirect.com/science/article/pii/S0926669025001682},
	doi = {10.1016/j.indcrop.2025.120622},
	abstract = {Chromosome segment substitution lines (CSSLs) represent a powerful genetic resource for quantitative trait loci (QTL) mapping, gene cloning and breeding. Here, we developed two sets of CSSLs consisting of 245 and 128 unique lines, which derived from OX2028 × K326 and Samsun × K326 crosses. On average, each CSSL carried 1.8 and 2.9 introgressed segments in the two sets, with an average physical segment length of approximately 34.3 Mb and 27.6 Mb, respectively. These CSSLs covered ∼97 \% and ∼77 \% of the genomes of OX2028 and Samsun, respectively. By performing QTL mapping based on best linear unbiased prediction (BLUP) of phenotypic traits, we identified a total of 64 QTLs associated with six agronomic traits and three disease resistance traits. These QTLs explained phenotypic variation ranging from 1.5 \% to 50.8 \%. Among them, 22 QTLs detected in OX2028 derived population and 42 detected in Samsun derived CSSLs. Notably, a new QTL for tobacco leaf width, qLW1–1 was narrowed down to an 8-Mb interval on chromosome 1, and NtZY01G00114, encoding an auxin-response factor protein, was considered as the candidate gene. Our study provides valuable genetic resources for tobacco breeding and enhances our understanding of the genetic basis of complex traits in tobacco.},
	urldate = {2026-05-19},
	journal = {Industrial Crops and Products},
	author = {Si, Huan and Wang, Dong and Zan, Yanjun and Liu, Wanfeng and Pu, Wenxuan and Li, Xiaoxu and Mao, Hui and Yang, Xingyou and Song, Shiyang and Wang, Yongda and Jiang, Caihong and Pan, Xuhao and Xiao, Zhiliang and Wen, Liuying and Sun, Yiwen and Liu, Dan and Cheng, Lirui and Yang, Aiguo},
	month = apr,
	year = {2025},
	keywords = {Agronomic traits, CSSLs, Disease resistance, QTL mapping, Tobacco},
	pages = {120622},
}

Chromosome segment substitution lines (CSSLs) represent a powerful genetic resource for quantitative trait loci (QTL) mapping, gene cloning and breeding. Here, we developed two sets of CSSLs consisting of 245 and 128 unique lines, which derived from OX2028 × K326 and Samsun × K326 crosses. On average, each CSSL carried 1.8 and 2.9 introgressed segments in the two sets, with an average physical segment length of approximately 34.3 Mb and 27.6 Mb, respectively. These CSSLs covered ∼97 % and ∼77 % of the genomes of OX2028 and Samsun, respectively. By performing QTL mapping based on best linear unbiased prediction (BLUP) of phenotypic traits, we identified a total of 64 QTLs associated with six agronomic traits and three disease resistance traits. These QTLs explained phenotypic variation ranging from 1.5 % to 50.8 %. Among them, 22 QTLs detected in OX2028 derived population and 42 detected in Samsun derived CSSLs. Notably, a new QTL for tobacco leaf width, qLW1–1 was narrowed down to an 8-Mb interval on chromosome 1, and NtZY01G00114, encoding an auxin-response factor protein, was considered as the candidate gene. Our study provides valuable genetic resources for tobacco breeding and enhances our understanding of the genetic basis of complex traits in tobacco.

@article{liu_origin_2025,
	title = {Origin and de novo domestication of sweet orange},
	volume = {57},
	copyright = {2025 The Author(s)},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/s41588-025-02122-4},
	doi = {10.1038/s41588-025-02122-4},
	abstract = {Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange. On the basis of a high-resolution haplotype-resolved genome analysis, we inferred that sweet orange originated from a sour orange × mandarin cross and confirmed this model using artificial hybridization experiments. We identified defense-related metabolites that potently inhibited the growth of multiple industrially important pathogenic bacteria. We introduced diversity to sweet orange, which showed wide segregation in fruit flavor and disease resistance and produced canker-resistant sweet orange by selecting defense-related metabolites. Our findings elucidate the origin of sweet orange and de novo domesticated disease-resistant sweet oranges, illuminating a strategy for the rapid domestication of perennial crops.},
	language = {en},
	number = {3},
	urldate = {2026-05-19},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Liu, Shengjun and Xu, Yuantao and Yang, Kun and Huang, Yue and Lu, Zhihao and Chen, Shulin and Gao, Xiang and Xiao, Gongao and Chen, Peng and Zeng, Xiuli and Wang, Lun and Zheng, Weikang and Liu, Zishuang and Liao, Guanglian and He, Fa and Liu, Junjie and Wan, Pengfei and Ding, Fang and Ye, Junli and Jiao, Wenbiao and Chai, Lijun and Pan, Zhiyong and Zhang, Fei and Lin, Zongcheng and Zan, Yanjun and Guo, Wenwu and Larkin, Robert M. and Xie, Zongzhou and Wang, Xia and Deng, Xiuxin and Xu, Qiang},
	month = mar,
	year = {2025},
	keywords = {Plant breeding, Plant genetics, Plant molecular biology},
	pages = {754--762},
}

Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange. On the basis of a high-resolution haplotype-resolved genome analysis, we inferred that sweet orange originated from a sour orange × mandarin cross and confirmed this model using artificial hybridization experiments. We identified defense-related metabolites that potently inhibited the growth of multiple industrially important pathogenic bacteria. We introduced diversity to sweet orange, which showed wide segregation in fruit flavor and disease resistance and produced canker-resistant sweet orange by selecting defense-related metabolites. Our findings elucidate the origin of sweet orange and de novo domesticated disease-resistant sweet oranges, illuminating a strategy for the rapid domestication of perennial crops.

@article{zan_genome_2025,
	title = {The genome and {GeneBank} genomics of allotetraploid {Nicotiana} tabacum provide insights into genome evolution and complex trait regulation},
	volume = {57},
	copyright = {2025 The Author(s)},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/s41588-025-02126-0},
	doi = {10.1038/s41588-025-02126-0},
	abstract = {Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker–trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.},
	language = {en},
	number = {4},
	urldate = {2026-05-19},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Zan, Yanjun and Chen, Shuai and Ren, Min and Liu, Guoxiang and Liu, Yutong and Han, Yu and Dong, Yang and Zhang, Yao and Si, Huan and Liu, Zhengwen and Liu, Dan and Zhang, Xingwei and Tong, Ying and Li, Yuan and Jiang, Caihong and Wen, Liuying and Xiao, Zhiliang and Sun, Yangyang and Geng, Ruimei and Ji, Yan and Feng, Quanfu and Wang, Yuanying and Ye, Guoyou and Fang, Lingzhao and Chen, Yong and Cheng, Lirui and Yang, Aiguo},
	month = apr,
	year = {2025},
	keywords = {Plant genetics, Plant sciences},
	pages = {986--996},
}

Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker–trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.