Genetic Diversity, Selection Signatures, and Genome-Wide Association Study Identify Candidate Genes Related to Litter Size in Hu Sheep

Abstract

Hu sheep is a renowned prolific local sheep breed in China, widely distributed across the country due to its excellent reproductive performance. Deciphering the molecular mechanisms underlying the high fecundity of Hu sheep is crucial for improving the litter size of ewes. In this study, we genotyped 830 female Hu sheep using the Illumina OvineSNP50 BeadChip and performed genetic diversity analysis, selection signature detection, and a genome-wide association study (GWAS) for litter size. Our results revealed that the Hu sheep population exhibits relatively high genetic diversity. A total of 4927 runs of homozygosity (ROH) segments were detected, with the majority (74.73%) being short in length. Different genomic inbreeding coefficients (F_ROH, F_HOM, F_GRM, and F_UNI) ranged from -0.0060 to 0.0126, showing low levels of inbreeding in this population. Additionally, we identified 91 candidate genomic regions through three complementary selection signature methods, including ROH, composite likelihood ratio (CLR), and integrated haplotype score (iHS), and annotated 189 protein-coding genes. Moreover, we observed two significant SNPs related to the litter size of Hu sheep using GWAS analysis based on a repeatability model. Integrating the selection signatures and the GWAS results, we identified 15 candidate genes associated with litter size, among which BMPR1B and UNC5C were particularly noteworthy. These findings provide valuable insights for improving the reproductive performance and breeding of high-fecundity lines of Hu sheep.

Keywords: GWAS; Hu sheep; candidate genes; genetic diversity; litter size; selection signatures.

Figure 1

PCA and genetic diversity analysis of female Hu sheep population. (A) PCA of the Hu sheep population; (B) Box plot of genetic diversity indices of Hu sheep. HO, observed heterozygosity; HE, expected heterozygosity; MAF, minor allele frequency; PIC, polymorphism information content; Ae, effective number of alleles; π, nucleotide diversity; (C) LD decay plot of Hu sheep; (D) The estimated effective population size of Hu sheep.

Figure 2

Distribution of ROHs in the Hu sheep population. (A) The frequency (bars) and average length (red line) of ROHs in different length categories; (B) The total length of ROHs and the total number of ROHs for per sheep; (C) The number of ROHs of different ROH length categories on each chromosome (bars) and the percentage of each chromosome covered by ROHs in the Hu sheep population (black line).

Figure 3

Scatterplots (bottom left) and Pearson’s correlations (top right) for eight different inbreeding coefficients in Hu sheep. ** denotes p-value < 0.01, *** denotes p-value < 0.001.

Figure 4

Manhattan plots of selection signatures detected by ROH (A), CLR (B), and iHS (C) methods in Hu sheep. The black dashed lines indicate the top 1% threshold.

Figure 5

Functional enrichment analysis of candidate genes simultaneously identified by at least two selection signature methods in Hu sheep. (A) GO. (B) KEGG.

Figure 6

The results of GWAS for litter size of Hu sheep. (A) Manhattan plot of the GWAS for litter size in Hu sheep. The black dashed line indicates the thresholds for litter size in Hu sheep (−log10(p-value) = 4.64). (B) QQ plot of GWAS for litter size in Hu sheep. (C) Sankey and dot plots showing the significantly enriched GO terms and KEGG pathways connected to candidate genes identified by GWAS for litter size in Hu sheep.