整合分析基因组和转录组学数据揭示华西牛胴体性状相关的候选变异

doi:10.1016/j.jia.2024.01.028

摘要/Abstract

摘要： 牛的胴体性状在肉牛产业中具有重要的经济意义。本研究基于华西牛资源群体，获得胴体性状表型、基因组和转录组数据，运用全基因组关联分析、表达数量性状基因座分析等策略，解析胴体性状功能变异的潜在分子机制。基于千牛计划公共数据对1566头华西牛芯片数据进行填充获得填充基因型数据，分别对胴体重、胴体长、胴体深、胴体胸深、屠宰率、净肉重和净肉率性状表型数据进行全基因关联分析，共鉴定到239个显著变异位点，注释到184个显著基因。采集资源群体中227头华西牛背最长肌组织进行转录组测序和分析，获得背最长肌组织中基因的表达量，综合考虑性别、批次、年龄校正后与对应的227头华西牛填充数据进行表达数量性状基因座分析，共鉴定到1,370,681个顺式调控变异和5,860个顺式调控基因，42,823个反式调控变异和734个反式调控基因，对顺式变异进一步精细定位发现，共有410个潜在因果变异。通过整合全基因组关联分析、顺式表达数量性状基因座分析和精细定位共鉴定到13个变异调控相同的基因，其中chr8:41889516为调控VLDLR基因的潜在因果变异。此外，我们利用227头背最长肌转录组数据、填充数据和全基因组关联分析的结果进行全转录组关联分析，鉴定出TTC30B、HMGA1、PRKD3和FXN基因分别与胴体胸深、胴体长、胴体重和屠宰率性状显著相关。本研究通过全基因组关联分析、表达数量性状基因座分析、精细定位和全转录组关联分析揭示了胴体性状的遗传特征，鉴定到与肉牛胴体性状相关的候选基因和变异，这些发现有助于深入了解胴体性状的遗传结构，并最终确定潜在基因和变异。

Abstract: Cattle carcass traits are economically important in the beef industry. In the present study, we identified 184 significant genes and 822 alternative genes for 7 carcass traits using genome-wide association studies (GWASs) in 1566 Huaxi beef cattle. We then identified 5,860 unique cis-genes and 734 trans-genes in 227 longissimus dorsi muscle (LDM) samples to better understand the genetic regulation of gene expression. Our integration study of the GWAS and cis-eQTL analysis detected 13 variants regulating 12 identical genes, in which one variant was also detected in fine-mapping analysis. Moreover, using a transcriptome-wide association study (TWAS), we identified 4 genes (TTC30B, HMGA1, PRKD3 and FXN) that were significantly related to carcass chest depth (CCD), carcass length (CL), carcass weight (CW) and dressing percentage (DP). This study identified variants and genes that may be useful for understanding the molecular mechanism of carcass traits in beef cattle.

Key words: Beef cattle , GWAS , , eQTL mapping , Fine mapping , , S-predixcan

. 整合分析基因组和转录组学数据揭示华西牛胴体性状相关的候选变异[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.01.028.

Yapeng Zhang, Wentao Cai, Qi Zhang, Qian Li, Yahui Wang, Ruiqi Peng, Haiqi Yin, Xin Hu, Zezhao Wang, Bo Zhu, Xue Gao, Yan Chen, Huijiang Gao, Lingyang Xu, Junya Li, Lupei Zhang. Integrated analyses of genomic and transcriptomic data reveal candidate variants associated with carcass traits in Huaxi cattle[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.01.028.

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