Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

被引:131
作者
Xu, Lingyang [1 ,2 ]
Bickhart, Derek M. [1 ]
Cole, John B. [1 ]
Schroeder, Steven G. [1 ]
Song, Jiuzhou [2 ]
Van Tassell, Curtis P. [1 ]
Sonstegard, Tad S. [1 ]
Liu, George E. [1 ]
机构
[1] ARS, Anim Genom & Improvement Lab, USDA, Beltsville, MD 20705 USA
[2] Univ Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 USA
基金
美国食品与农业研究所;
关键词
cattle genome; population structure; positive selection; haplotype network; RECENT POSITIVE SELECTION; GROWTH-HORMONE RECEPTOR; ARTIFICIAL SELECTION; BOS-TAURUS; WIDE ASSOCIATION; LINKAGE DISEQUILIBRIUM; STATISTICAL-METHOD; COMPLEX TRAITS; BIRTH-WEIGHT; DAIRY-CATTLE;
D O I
10.1093/molbev/msu333
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.
引用
收藏
页码:711 / 725
页数:15
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