Genome-Wide Specific Selection in Three Domestic Sheep Breeds

Huihua Wang; Li Zhang; Jiaxve Cao; Mingming Wu; Xiaomeng Ma; Zhen Liu; Ruizao Liu; Fuping Zhao; Caihong Wei; Lixin Du

doi:10.1371/journal.pone.0128688

Genome-Wide Specific Selection in Three Domestic Sheep Breeds

PLoS One. 2015 Jun 17;10(6):e0128688. doi: 10.1371/journal.pone.0128688. eCollection 2015.

Authors

Huihua Wang¹, Li Zhang¹, Jiaxve Cao¹, Mingming Wu¹, Xiaomeng Ma¹, Zhen Liu¹, Ruizao Liu¹, Fuping Zhao¹, Caihong Wei¹, Lixin Du¹

Affiliation

¹ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China, Beijing, China.

Abstract

Background: Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.

Results: We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study.

Conclusions: Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Body Weight
Breeding*
Genetic Loci
Genome*
Genome-Wide Association Study
Hybridization, Genetic
Meat*
Phenotype
Selection, Genetic
Sheep
Sheep, Domestic / classification
Sheep, Domestic / genetics*

Grants and funding

This research was supported by the National Key Technology R&D Program of China (2011BAD28B05-2)(http://www.most.gov.cn/eng/index.htm). LZ received funding from the Chinese Academy of Agricultural Sciences(2014ywf-yb-7) (http://en.gscaas.net.cn/). The funder had collected and analyzed data, and decided to publish.