Abstract
Yunnan semi-fine wool sheep are among the most important cultivated sheep breeds in China. However, their population structure, genetic characteristics and traits of interest are poorly studied. In this study, we systematically studied the population characteristics and selection signatures of 40 Yunnan semi-fine wool sheep using SNPs obtained from whole-genome resequencing data. A total of 1393 Gb of clean data were acquired. The mapping rate against the reference genome was 91.23% on average (86.01%–92.26%), and the average sequence depth was 9.51X. After filtering, 28,593,198 SNPs and 4,725,259 indels with high quality were obtained. The heterozygosity rate, inbreeding coefficient and effective population size of the sheep were calculated to preliminarily explore their genetic characteristics. The average heterozygosity rate was 0.264, the average inbreeding coefficient was 0.0099, and the effective population size estimated from the heterozygote excess (HE) was 242.9. Based on the Tajima’s D and integrated haplotype score (iHS) approaches, 562 windows and 11,356 core SNPs showed selection signatures in the Yunnan semi-fine wool sheep population. After genome annotation and gene enrichment analysis, we found traces of early domestication in sensory organs, behavioural activity and the nervous system as well as adaptive changes in reproductive and wool traits under selection in this population. Some selected genes related to litter size, including FSHR, BMPR1B and OXT, were identified as being under selection. Specific missense mutations of the FSHR gene that differed from the reference genome were also identified in the population, and we found some SNP variations that may affect litter size. Our findings provide a theoretical basis for the conservation and utilization of Yunnan semi-fine wool sheep. Furthermore, our results reveal some changes common to sheep after domestication and provide a new opportunity to investigate the genetic variation influencing fecundity within a population evolving under artificial selection.
Highlights
Yunnan semi-fine wool sheep are among the most important cultivated breeds in Yunnan Province, China
The objectives of this study were to explore the population characteristics and genetic structure of Yunnan semi-fine wool sheep, to screen selection regions related to important traits and to identify variants by using genome-wide selection signature detection
The sequencing data of 4 Zhaotong sheep and 3 Romney sheep were downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to further explore the population structure of Yunnan semi-fine wool sheep
Summary
Yunnan semi-fine wool sheep are among the most important cultivated breeds in Yunnan Province, China. This breed has excellent wool quality, high adaptability and strong robustness. In 2000, this breed was approved by the Chinese Livestock and Poultry Breed Approval Committee, becoming the first approved breed of coarse semi-fine wool sheep in China. Yunnan semi-fine wool sheep are medium in body size, and their wool quality is comparable to that of Romney and Lincoln sheep. Due to its competitive advantages and rapid adaptation to the local environment, the population of Yunnan semi-fine wool sheep has been continuously expanded, with the population size exceeding 100,000 individuals in 2005 (Yuan and Sun, 2014). The improvement of reproductive traits is important for Yunnan semi-fine wool sheep
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