Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus

IF 8.3 1区 生物学 Q1 PLANT SCIENCES New Phytologist Pub Date : 2024-08-21 DOI:10.1111/nph.20026
Mengjun Shu, Timothy B. Yates, Cai John, Anne E. Harman-Ware, Renee M. Happs, Nathan Bryant, Sara S. Jawdy, Arthur J. Ragauskas, Gerald A. Tuskan, Wellington Muchero, Jin-Gui Chen
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利用杨树的 eQTL 调控和共表达网络为 GWAS 结果提供生物学背景。
我们的研究利用全基因组关联研究(GWAS)将核苷酸变异与毛白杨(Populus trichocarpa)的性状联系起来,毛白杨是一种关联不平衡迅速衰减的物种。我们的目的是克服在没有足够生物背景的情况下解释单个位点的统计关联所带来的挑战,这种挑战往往导致我们仅仅依赖于来自无关模式生物的基因注释。我们采用了一种综合方法,包括使用三种单独的木质纤维素表型技术进行针对多个性状的全球基因组分析、表达定量性状位点(eQTL)分析以构建围绕每个候选位点的转录调控网络,以及共表达分析为这些网络提供生物学背景,并以毛白杨的木质纤维素生物合成为案例进行研究。研究发现了三个可能参与木质纤维素形成的候选基因,其中包括一个以前被认可的基因(Potri.005G116800/VND1,次生细胞壁形成的关键调节因子)和两个新发现的在木质纤维素生物合成中可能发挥作用的基因(Potri.012G130000/AtSAP9 和 Potri.004G202900/BIC1)。我们的综合方法为提供与性状变异相关的基因座的生物学背景提供了一个框架,有助于发现新的基因和调控网络。
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来源期刊
New Phytologist
New Phytologist 生物-植物科学
自引率
5.30%
发文量
728
期刊介绍: New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.
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