Genome-Wide Association Analysis of Growth Traits in Hu Sheep

Abstract

(1) Background: The Hu sheep is a renowned breed characterized by high reproduction, year-round estrus, and resistance to high humidity and temperature conditions. However, the breed exhibits lower growth rates and meat yields, which necessitate improvements through selective breeding. The integration of molecular markers in sheep breeding programs has the potential to enhance growth performance, reduce breeding cycles, and increase meat production. Currently, the applications of SNP chips for genotyping in conjunction with genome-wide association studies (GWAS) have become a prevalent approach for identifying candidate genes associated with economically significant traits in livestock. (2) Methods: To pinpoint candidate genes influencing growth traits in Hu sheep, we recorded the birth weight, weaning weight, and weights at 3, 4, 5, 6, and 7 months for a total of 567 Hu sheep, and genotyping was performed using the Ovine 40K SNP chip. (3) Results: Through GWAS analysis and KEGG pathway enrichment, we identified three candidate genes associated with birth weight (CAMK2B, CACNA2D1, and CACNA1C). Additionally, we found two candidate genes linked to weaning weight (FGF9 and BMPR1B), with CACNA2D1 also serving as a shared gene between birth weight and weaning weight traits. Furthermore, we identified eight candidate genes related to monthly weight (FIGF, WT1, KCNIP4, JAK2, WWP1, PLCL1, GPRIN3, and CCSER1). (4) Conclusion: Our findings revealed a total of 13 candidate genetic markers that can be utilized for molecular marker-assisted selection, aiming to improve meat production in sheep breeding programs.

Keywords: GWAS; Hu sheep; Ovine 40K SNP chip; candidate genes; growth.

Figure 1

(a) SNP number of each chromosome before and after quality control. Chr: chromosome; Before_QC: SNP number of each chromosome before quality control; After_QC: SNP number of each chromosome after quality control; (b–h) Phenotypic distribution of the body weight measured at: (b) Birth weight; (c) Weaning weight; (d) 3-month weight; (e) 4-month weight; (f) 5-month weight; (g) 6-month weight; (h) 7-month weight; (i) PCA result of population stratification of Hu sheep.

Figure 2

Manhattan plots of genome-wide association studies and corresponding Q_Q plots results for body weight of Hu sheep. The x-axis represents the chromosomes, and the y-axis represents the −log10 (p-value). Different colors indicate various chromosomes. The Q_Q plots show the observed vs. expected log p-value. (a) Birth weight; (b) Weaning weight; (c) 3-month weight; (d) 4-month weight; (e) 5-month weight; (f) 6-month weight; (g) 7-month weight.

Figure 3

KEGG pathway for genes related to body weight. (a) Birth weight; (b) Weaning weight; (c) Monthly weight.