Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep

Abstract

Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10^-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.

Keywords: Chinese sheep; genetic diversity; inbreeding coefficients; runs of homozygosity; selection signature; whole-genome sequencing; wool.

Figure 1

Population structure and genetic relationships among 6 domestic sheep breeds (n = 119) and 20 Asiatic mouflons (AMU). (a) Neighbor-joining (NJ) phylogenetic tree illustrating relationships among the six domestic sheep breeds (LSS: Liangshan semi-fine-wool sheep, LST: Border Leicester, RMN: Romney, CNM: Chinese Merino sheep, TIB: Tibetan sheep, and YNS: Yunnan sheep) and wild sheep. (b) Principal component analysis of all 139 sampled sheep. (c) Model-based clustering of sheep breeds using ADMIXTURE with K = 6. (d) The outgroup-f3 analysis of LSS with LST, RMN, CNM, TIB, and YNS, with AMU as an outgroup.

Figure 2

Summary of linkage disequilibrium (LD) and runs of homozygosity (ROH) detected in the sheep autosomal genome. (a) The genome-wide average LD decay estimated from each breed. (b) The proportions of the ROH total number with different length classes in LSS. (c) The summary of the total ROH number and length in the genome of each individual in LSS. (d) The distribution of the total ROH number and length across autosomes in LSS.

Figure 3

Genomic inbreeding coefficients in LSS were estimated using five different methods. (a) Boxplot displaying estimated genomic inbreeding coefficients in LSS. (b) Heatmap showing Pearson’s correlations among genomic inbreeding coefficients in LSS based on five methods.

Figure 4

Genome-wide selection signals of LSS. Manhattan plot of genome-wide cross-population extended haplotype homozygosity (XP-EHH) (a), cross-population composite likelihood ratio (XP-CLR) (b), and F_ST (c) across all 26 autosomes between LSS and TIB sheep. (d) The enriched gene ontology (GO) biological processes for the genes overlapping with XP-EHH. (e) Venn diagram for the selected genes identified via three approaches.

Figure 5

Summary of three examples of selective sweep regions. Three selection signals encompass IRF2BP2 on Chromosome 25 (a), ALOX5 on Chromosome 25 (b), and BVES on Chromosome 8 (c), respectively. These putative sweep regions were further validated by XP-EHH and F_ST values. Annotations of genes within the sweep region and SNPs fixed for reference alleles in LSS were provided. The distribution of allele frequencies at mutation sites in the three genes is shown at the bottom.