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Genome-wide association study of growth and reproductive traits based on low-coverage whole-genome sequencing in a Chubao black-head goat population

文献类型： 外文期刊

作者： Shangguan, Aishao 1 ; Xiang, Chong 2 ; Deng, Zhao 1 ; Zhang, Nian 1 ; Yu, Min 4 ; Zhang, Feng 1 ; Suo, Xiaojun 1 ; Chen, Mingxin 1 ; Chen, Can 2 ; Tao, Hu 1 ; Xiong, Qi 1 ;

作者机构： 1.Hubei Acad Agr Sci, Inst Anim Sci & Vet Med, Hubei Key Lab Anim Embryo Engn & Mol Breeding, Wuhan 430064, Peoples R China

2.Changjiang Polytech, Inst Data Informat, Wuhan 430074, Peoples R China

3.Huazhong Agr Univ, Minist Educ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Wuhan 430070, Peoples R China

4.China Univ Geosci, Human Resources Dept, Wuhan 430074, Peoples R China

关键词： Growth traits; Reproductive traits; Low-coverage whole-genome sequencing; Genome-wide association study; Chubao black-head goats

期刊名称：GENE （ 影响因子：2.4； 五年影响因子：2.8 ）

ISSN： 0378-1119

年卷期： 2024 年 931 卷

页码：

收录情况： SCI

摘要： The Chubao black-head goat is a novel hybrid breed that combines the advantages of Macheng black goats, such as good reproductive performance, strong adaptability, and resistance to rough feeding, with the superior growth and meat characteristics of Boer goats. Given the substantial economic importance of growth (such as birth weight, body height, body length, and chest circumference across different growth stages) and reproductive traits (particularly average litter size after first parity), the aim of this study was to identify significant SNPs and candidate genes associated with these traits in Chubao black-head goats. Through whole-genome sequencing (with 34 goats at approximately 15x coverage and 466 goats at approximately 1x coverage), genotype imputation, and quality control, 22,665,331 SNPs were identified and subsequently used for genetic analyses. Heritability estimates indicated that growth traits exhibit moderate to high heritability (ranging from 0.297 +/- 0.071 to 0.535 +/- 0.118), while reproductive traits demonstrated low to moderate heritability (with a value of 0.220 +/- 0.108). By performing FarmCPU-based genome-wide association studies, we identified 48 potentially significant SNPs associated with growth traits and 7 with reproductive traits. Additionally, 85 candidate genes (such as COL14A1, ZNF148, and TTC39C) linked to growth traits were identified and enriched in pathways associated with fundamental molecular biological activities such as protein deubiquitination, regulation of mRNA stability, and the MAPK signaling pathway. Furthermore, 10 candidate genes (such as SOHLH2, CCNA2, and SOX7) associated with reproductive traits were identified and enriched in pathways related to specific reproductive processes such as oocyte differentiation, endoderm formation, and progesterone-mediated oocyte maturation. Overall, these findings provide valuable preliminary insights into the molecular mechanisms underlying growth and reproductive traits in Chubao black-head goats. However, further functional validation is needed to effectively use these potential SNPs and candidate genes in improving the breeding of these traits in this breed.

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