Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Ministry of Agriculture, China Agricultural University, Beijing, China.
PLoS One. 2013;8(3):e60440. doi: 10.1371/journal.pone.0060440. Epub 2013 Mar 28.
Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and then verified the biological significance of these identified regions based on commonly-used bioinformatics analyses. Results showed a total of 125 significant regions in entire genome containing some of important functional genes such as LEP, ABCG2, CSN1S1, CSN3 and TNF based on the Gene Ontology database. Some of these annotated genes involved in the core regions overlapped with those identified in our previous GWAS as well as those involved in a recently constructed candidate gene database for cattle, further indicating these genes under positive selection maybe underlie milk production traits and other important traits in Chinese Holstein. Furthermore, in the enrichment analyses for the second level GO terms and pathways, we observed some significant terms over represented in these identified regions as compared to the entire bovine genome. This indicates that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests. Findings in our study could help detect functional candidate genes under positive selection for further genetic and breeding research in Chinese Holstein.
全基因组的选择信号可以帮助我们理解选择的机制，并为育种计划找到因果变异的目标。在本研究中，我们对中国荷斯坦牛进行了扩展单倍型纯合度（EHH）测试，以鉴定具有这些信号的显著核心区域，然后基于常用的生物信息学分析来验证这些鉴定区域的生物学意义。结果表明，在整个基因组中，共鉴定到 125 个显著的核心区域，这些区域包含了一些重要的功能基因，如 LEP、ABCG2、CSN1S1、CSN3 和 TNF 等，这些基因都与基因本体数据库（GO）中的注释基因相关。这些核心区域中的一些注释基因与我们之前的 GWAS 以及最近构建的牛候选基因数据库中鉴定到的基因重叠，这进一步表明这些受正向选择的基因可能与中国荷斯坦牛的产奶性状和其他重要性状有关。此外，在二级 GO 术语和途径的富集分析中，与整个牛基因组相比，这些鉴定区域中存在一些显著的代表性术语。这表明，一些与产奶性状相关的功能基因，如 GO 术语所反映的，可以聚集在核心区域，这为 EHH 测试鉴定的核心区域的可利用性提供了有前景的证据。我们的研究结果可以帮助检测受正向选择影响的功能候选基因，为中国荷斯坦牛的进一步遗传和育种研究提供帮助。
