Maxman Gomo, van Marle-Köster Este, Lashmar Simon Frederick, Visser Carina
Department of Animal Science, Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
Animal Production, Agricultural Research Council, Pretoria, South Africa.
Trop Anim Health Prod. 2024 Dec 27;57(1):13. doi: 10.1007/s11250-024-04265-8.
In the present study 1,709 cattle, including 1,118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150 K bovine SNP panel. A genomic data set of 122,632 quality-filtered single nucleotide polymorphisms (SNPs) were used to identify selection signatures within breeds based on conserved runs of homozygosity (ROH) and heterozygosity (ROHet) estimated with the detectRUNS R package. The mean number of ROH per animal varied across breeds ranging from 36.09 ± 12.82 (NGI) to 51.82 ± 21.01 (DRB), and the mean ROH length per breed ranged between 2.31 Mb (NGI) and 3.90 Mb (DRB). The smallest length categories i.e., ROH < 4 Mb were most frequent, indicating historic inbreeding effects for all breeds. The ROH based inbreeding coefficients (F) ranged between 0.033 ± 0.024 (NGI) and 0.081 ± 0.046 (DRB). Genes mapped to candidate regions were associated with immunity (ADAMTS12, LY96, WDPCP) and adaptation (FKBP4, CBFA2T3, TUBB3) in cattle and genes previously only reported for immunity in mice and human (EXOC3L1, MYO1G). The present study contributes to the understanding of the genetic mechanisms of adaptation, providing information for potential molecular application in genetic evaluation and selection programs.
在本研究中，使用GeneSeek®基因组分析器™150K牛单核苷酸多态性（SNP）面板对1709头牛进行了基因分型，其中包括1118头德拉肯斯伯格牛（DRB）、377头恩古尼牛（NGI）和214头图利牛（TUL）。利用detectRUNS R软件包估计的纯合性连续区域（ROH）和杂合性连续区域（ROHet），对122632个经过质量筛选的单核苷酸多态性（SNP）的基因组数据集进行分析，以识别各品种内的选择信号。每头动物的ROH平均数因品种而异，范围从36.09±12.82（NGI）到51.82±21.01（DRB），每个品种的ROH平均长度在2.31 Mb（NGI）和3.90 Mb（DRB）之间。最小长度类别即ROH<4 Mb最为常见，这表明所有品种都存在历史近亲繁殖效应。基于ROH的近亲繁殖系数（F）在0.033±0.024（NGI）和0.081±0.046（DRB）之间。定位到候选区域的基因与牛的免疫（ADAMTS12、LY96、WDPCP）和适应性（FKBP四、CBFA2T3、TUBB3）相关，以及先前仅在小鼠和人类中报道过的免疫相关基因（EXOC3L1、MYO1G）。本研究有助于理解适应的遗传机制，为遗传评估和选择计划中的潜在分子应用提供信息。
