Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments

Abstract

Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (FST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by FST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.

Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

“…Therefore, it is beneficial to consider our results in historical demographic context of Chinese sheep population. This finding is in line with our previous studies of genomic diversity, population structure and selection signature, in which we observed that principal component and admixture analysis clustered population corresponding to their geographical distribution and breeding history [ 45 ]. In general, the increase of the estimated N e value across five sheep breeds generations ago suggest that these animals can ensure viability within breeds in breeding programs [ 58 ].…”

“…In previous studies, we revealed the genomic diversity, population structure and selection signature characteristics of five sheep populations in China [ 45 ]. Here, we extended our analysis using runs of homozygosity, LD and N e as useful tools for detecting genomic relatedness, providing population assessment historical information over time and predicting underlying genome architecture [ 46 ].…”

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

“…The use of multiple methods reduces the chance of false positive results. In this study, there were many overlapping regions identified between at least two approaches ( Supplementary Table 5 ), which provides stronger evidence of selection for specific traits ( Hohenlohe et al, 2010 ; Oleksyk et al, 2010 ; Abied et al, 2020 ). It is worth mentioning that the use of different methods can result in the identification of different regions ( Fariello et al, 2013 ), as methods might be based on different source of information (e.g., single-SNP allele frequency or haplotype structure).…”

Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

“…Local sheep breeds traditionally raised under extreme environments are an excellent model for studying genetic adaptation [ 4 ]. Under these conditions, selective breeding for improved (re)productive performance is limited or non-existent, leaving natural selection as the primary evolutionary acting mechanism.…”