Abstract
Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.
Highlights
Modern sheep (Ovis aries) were domesticated in the Fertile Crescent region of the Near East approximately 8,000–9,000 years ago [1]
Genetic diversity and population structure analysis of sheep using genome-wide single nucleotide polymorphisms (SNPs) showed that they might be divided into two genetic groups [4], that is, the thin (Tibetan group) and the fat (Mongolian and Kazakh group) types
According to the positional annotation, all these SNPs were located within intergenic regions (9.068%), exons (0.826%), introns (36.229%), ncRNA transcript regions (36.560%), and 50/30 untranslated regions (UTRs; 0.771%)
Summary
Modern sheep (Ovis aries) were domesticated in the Fertile Crescent region of the Near East approximately 8,000–9,000 years ago [1]. The comprehensive analysis by genotyping 50K single nucleotide polymorphism in 2,819 animals from 74 worldwide sheep breeds revealed that they had maintained a relatively high genetic diversity in comparison with other main farm animals [2]. China has relatively abundant sheep genetic resources composed of at least officially recognized breeds and many local populations [3]. Genetic diversity and population structure analysis of sheep using genome-wide SNPs showed that they might be divided into two genetic groups [4], that is, the thin (Tibetan group) and the fat (Mongolian and Kazakh group) types. A large number of sheep breeds are widely distributed in a diverse range of environments with considerable genetic and morphological variation
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