数字农科院2.0

TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean

文献类型： 外文期刊

作者： Li, Delin;Wang, Qi;Tian, Yu;Lyv, Xiangguang;Zhang, Hao;Hong, Huilong;Gao, Huawei;Li, Yan-Fei;Zhao, Chaosen;Wang, Jiajun;Wang, Ruizhen;Yang, Jinliang;Liu, Bin;Schnable, Patrick S.;Schnable, James C.;Li, Ying-Hui;Qiu, Li-Juan

作者机构：

关键词： eQTLs;TWAS;structural variation;alternative splicing;soybean

期刊名称： PLANT COMMUNICATIONS

ISSN： 2590-3462

年卷期： 2024 年 5 卷 10 期

页码：

收录情况： SCIE（2024版） ; ; CSCD（2023-2024年度）

摘要： A genome-wide association study (GWAS) identifies trait-associated loci, but identifying the causal genes can be a bottleneck, due in part to slow decay of linkage disequilibrium (LD). A transcriptome-wide association study (TWAS) addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay. We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29 286 soybean genes. Different TWAS solutions were less affected by LD and were robust to the source of expression, identifing known genes related to traits from different tissues and developmental stages. The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing. By introducing a new exon proportion feature, we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing. As a result, the genes identified through our TWAS approach exhibited a diverse range of causal variations, including SNPs, insertions or deletions, gene fusion, copy number variations, and alternative splicing. Using this approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously been linked to this trait, providing insights complementary to those from GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.

分类号：

  • 相关文献

[1]GmSop20 Functions as a Key Coordinator of the Oil-To-Protein Ratio in Soybean Seeds. Zheng, Haowei,Feng, Xinkang,Wang, Longlong,Shao, Wentao,Guo, Shiyu,Zhao, Duo,Li, Jiajia,Yan, Long,Miao, Long,Sun, Bincheng,Gao, Huihui,Qiu, Hongmei,Hu, Yu,Kong, Linlin,Stupar, Robert M.,Li, Ying-hui,Qiu, Li-juan,Wang, Xiaobo. 2025

[2]Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton. Ma, Jianjiang,Jiang, Yafei,Pei, Wenfeng,Wu, Man,Ma, Qifeng,Liu, Ji,Song, Jikun,Jia, Bing,Liu, Shang,Wu, Jianyong,Zhang, Jinfa,Yu, Jiwen. 2022

[3]Cis-eQTLs in seven duck tissues identify novel candidate genes for growth and carcass traits. Wentao Cai,Jian Hu,Yunsheng Zhang,Zhanbao Guo,Zhengkui Zhou,Shuisheng Hou. 2024

[4]Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues. Liyan Deng,Marta Gòdia,Martijn F.L. Derks,Barbara Harlizius,Samin Farhangi,Zhonglin Tang,Martien A.M. Groenen,Ole Madsen. 2025

[5]Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle. Mang Liang,Bingxing An,Tianyu Deng,Lili Du,Keanning Li,Sheng Cao,Yueying Du,Lingyang Xu,Lupei Zhang,Xue Gao,Yang Cao,Yuming Zhao,Junya Li,Huijiang Gao. 2023

[6]Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition. Xiao Han,Chenxu Gao,Lisen Liu,Yihao Zhang,Yuying Jin,Qingdi Yan,Lan Yang,Fuguang Li,Zhaoen Yang. 2022

[7]The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle. Cai, Wentao,Zhang, Yapeng,Chang, Tianpeng,Wang, Zezhao,Zhu, Bo,Chen, Yan,Gao, Xue,Xu, Lingyang,Zhang, Lupei,Gao, Huijiang,Song, Jiuzhou,Li, Junya. 2023

[8]Population-level gene expression can repeatedly link genes to functions in maize. Torres-Rodriguez, J. Vladimir,Li, Delin,Turkus, Jonathan,Newton, Linsey,Davis, Jensina,Lopez-Corona, Lina,Ali, Waqar,Sun, Guangchao,Mural, Ravi V.,Grzybowski, Marcin W.,Zamft, Bradley M.,Thompson, Addie M.,Schnable, James C.. 2024

[9]Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers. Aixin Ni,Henk Bovenhuis,Mario P.L. Calus,Yunlei Li,Jingwei Yuan,Yanyan Sun,Jilan Chen. 2025

[10]Origin and evolution of the kiwifruit Y chromosome. Yue, Junyang,Chen, Qinyao,Zhang, Sijia,Lin, Yunzhi,Ren, Wangmei,Li, Bingjie,Wu, Ying,Wang, Yingzhen,Zhou, Yongfeng,Liu, Yongsheng. 2023

[11]Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum). Xiaoyang Wang,Yuchen Miao,Yingfan Cai,Gaofei Sun,Yinhua Jia,Song Song,Zhaoe Pan,Yuanming Zhang,Liyuan Wang,Guoyong Fu,Qiong Gao,Gaoxiang Ji,Pengpeng Wang,Baojun Chen,Zhen Peng,Xiaomeng Zhang,Xiao Wang,Yi Ding,Daowu Hu,Xiaoli Geng,Liru Wang,Baoyin Pang,Wenfang Gong,Shoupu He,Xiongming Du. 2021

[12]Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. Jie Ma,Hua Wei,Xiaoman Yu,Yang Lv,Yu Zhang,Qian Qian,Lianguang Shang,Longbiao Guo. 2022

[13]Multiple variation patterns of terpene synthases in 26 maize genomes. Sun Y.,Xiao W.,Wang Q.-N.,Wang J.,Kong X.-D.,Ma W.-H.,Liu S.-X.,Ren P.,Xu L.-N.,Zhang Y.-J.. 2023

[14]Five improved sesame reference genomes and genome resequencing unveil the contribution of structural variants to genetic diversity and yield-related traits variation. Song, Shengnan,Dossou, Senouwa Segla Koffi,Meng, Minghui,Sheng, Chen,Li, Huan,Zhou, Rong,Li, Donghua,Xu, Pan,You, Jun,Wang, Linhai. 2023

[15]Genomes of single- and double-petal jasmines (Jasminum sambac) provide insights into their divergence time and structural variations. Wang, Pengjie,Fang, Jingping,Lin, Hongzheng,Yang, Wenwen,Yu, Jiaxin,Hong, Yaping,Jiang, Mengwei,Gu, Mengya,Chen, Qinchang,Zheng, Yucheng,Liao, ZhenYang,Chen, Guixin,Yang, Jiangfan,Jin, Shan,Zhang, Xingtan,Ye, Naixing. 2022

[16]Chromosome-level genome assembly of a regenerable maize inbred line A188. Guifang Lin,Cheng He,Jun Zheng,Dal-Hoe Koo,Ha Le,Huakun Zheng,Tej Man Tamang,Jinguang Lin,Yan Liu,Mingxia Zhao,Yangfan Hao,Frank McFraland,Bo Wang,Yang Qin,Haibao Tang,Donald R. McCarty,Hairong Wei,Myeong-Je Cho,Sunghun Park,Heidi Kaeppler,Shawn M. Kaeppler,Yunjun Liu,Nathan Springer,Patrick S. Schnable,Guoying Wang,Frank F. White,Sanzhen Liu. 2021

[17]Evolutionary Genomics Of Structural Variation In Asian Rice (Oryza Sativa) Domestication. Kou, YX, Liao, Y, Toivainen, T, Lv, YD, Tian, XM, Emerson, JJ, Gaut, BS, Zhou, YF. 2020

[18]Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops. Han Z.,Li F.,Qiao W.,Zheng X.,Cheng Y.,Zhang L.,Huang J.,Wang Y.,Lou D.,Xing M.,Fan W.,Nie Y.,Guo W.,Wang S.,Liu Z.,Yang Q.. 2023

[19]Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Xiaoting Xia,Fengwei Zhang,Shuang Li,Xiaoyu Luo,Lixin Peng,Zheng Dong,Hubert Pausch,Alexander S. Leonard,Danang Crysnanto,Shikang Wang,Bin Tong,Johannes A. Lenstra,Jianlin Han,Fuyong Li,Tieshan Xu,Lihong Gu,Liangliang Jin,Ruihua Dang,Yongzhen Huang,Xianyong Lan,Gang Ren,Yu Wang,Yuanpeng Gao,Zhijie Ma,Haijian Cheng,Yun Ma,Hong Chen,Weijun Pang,Chuzhao Lei,Ningbo Chen. 2023

[20]Adaptive and maladaptive introgression in grapevine domestication. Hua Xiao,Zhongjie Liu,Nan Wang,Qiming Long,Shuo Cao,Guizhou Huang,Wenwen Liu,Yanling Peng,Summaira Riaz,Andrew M. Walker,Brandon S. Gaut,Yongfeng Zhou. 2023

作者其他论文 更多>>