Taye Mengistie, Yoon Joon, Dessie Tadelle, Cho Seoae, Oh Sung Jong, Lee Hak-Kyo, Kim Heebal
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
College of Agriculture and Environmental Sciences, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia.
Genes Genomics. 2018 Jan;40(1):63-75. doi: 10.1007/s13258-017-0610-z. Epub 2017 Sep 30.
Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.
针对所需表型/性状的人工选择极大地改变了家畜的基因组，从而产生了在形态、生产和环境适应性状上有很大差异的品种。安格斯牛是为了获得优质牛肉而培育出的著名牛品种之一。本文旨在探索安格斯牛中与肉质性状及其他相关表型有关的受选择基因组区域。使用跨群体复合似然比（XP-CLR）统计方法，将10头安格斯牛的全基因组与11头韩牛（A-H）和9头泽西牛（A-J）品种进行了比较。将经验分布的前1%视为显著，并使用UMD3.1进行注释。结果显示，从A-H和A-J比较中分别发现了255个和210个处于选择中的基因。WebGestalt基因本体分析得出了16条（A-H）和5条（A-J）显著富集的KEGG通路。一些与肉质性状（胰岛素信号传导、II型糖尿病通路、粘着斑通路和细胞外基质-受体相互作用）以及饲养效率（嗅觉转导、紧密连接和代谢通路）相关的通路得到了富集。发现影响牛肉品质性状（如FABP3、FTO、DGAT2、ACS、ACAA2、CPE、TNNI1）、身高和体型（如PLAG1、LYN、CHCHD7、RPS20）、繁殖力和难产（如ESR1、RPS20、PPP2R1A、GHRL、PLAG1）、饲养效率（如PIK3CD、DNAJC28、DNAJC3、GHRL、PLAG1）、毛色（如MC1-R）和遗传疾病（如ITGB6、PLAG1）的基因在安格斯牛中受到正选择。该研究确定了与安格斯牛的肉质性状及其他表型相关的基因和通路。本研究的结果在使用额外或独立数据集进行验证后，将为安格斯牛特别是一般肉牛的研究提供有用信息。
