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. 2025 Jan 14;26(1):37.
doi: 10.1186/s12864-024-11097-1.

Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat

Mingxuan Han #  1 , Xinbo Wang #  1 , Haidong Du  2 , Yanlong Cao  2 , Zhanqiang Zhao  2 , Shuran Niu  1 , Xuxu Bao  1 , Youjun Rong  1 , Xiaofang Ao  1 , Furong Guo  1 , Qincheng Xia  1 , Fangzheng Shang  1 , Ruijun Wang  3   4   5 , Yanjun Zhang  6   7   8
Affiliations

Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat

Mingxuan Han et al. BMC Genomics. .

Abstract

Background: Identifying markers or genes crucial for growth traits in Zhongwei goats is pivotal for breeding. Pinpointing genetic factors linked to body size gain enhances breeding efficiency and economic value. In this study, we used the MGISEQ-T7 platform to re-sequence 240 Zhongwei goats (133 male; 107 female) belonging to 5 metrics of growth traits at different growth stages (40 days and 6 months, here in after referred to as 40d and 6 m), namely, Body Weight (BW), Body Height (BH), Body Length (BL), Chest Circumference (CC), Tube Circumference (TC) were examined. A Genome-wide association study (GWAS) was conducted to identify candidate genes associated with the five indicators of body conformation traits, thereby establishing a foundation for subsequent investigations into the biological functions of these genes.

Results: A total of 19.89 Tb of raw data was generated with an average sequencing depth of about 20×. After quality control, 15,958,716 SNPs were available for the analysis. A total of 342 genome-wide significant SNPs were obtained. Among them, in the two physiological stages of 40d and 6 m, 147 and 32 SNPs were significantly associated with BW; 1 and 4 SNPs were significantly associated with BH; 19 and 6 SNPs were significantly associated with BL; 33 and 64 SNPs were significantly associated with CC, 34 and 2 SNPs were significantly associated with TC. These SNPs were annotated to 425 candidate genes. Finally, A total of 39 candidate genes are closely related to biological processes such as skeletal muscle development, skeletal formation, carcass quality, and embryonic development, where ADIPOQ, CCDD39, PTPRT, ZNF215, VRTN, ABCD4, DLST, ADAMTS2, ROBO1, AKAP13, AQPI, SOX2, and AHSG were identified as an important component of the genetic framework that may control somatic conformational traits in Zhongwei goats. which warrants further investigation and review. We verified the polymorphism of 11 SNPs by KASP, and found that Chr13_g.11,700,438 A > G, Chr15_g.37,120,328 A > G, Chr6_g.7,209,383 C > T, Chr20_g.51277932T > A, Chr19_g.17,078,199 A > G, and Chr1_g.79,943,276 C > T were significantly genotyped in verified populations (P < 0.001).

Conclution: It is the first GWAS study to analyze genomic data from 40d and 6 m of Zhongwei goats to understand the molecular genetic mechanisms of growth. Our research identified a series of SNPs and candidate genes associated with growth traits, which could assist us in developing the meat production trait in Zhongwei goats.

Keywords: Body conformation traits; GWAS; KASP validation; Re-sequence; Zhongwei goat.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: All samples were collected in accordance with the International Guiding Principles for Biomedical Research involving animals and approved by the Special Committee on Scientific Research and Academic Ethics of Inner Mongolia Agricultural University, responsible for the approval of Biomedical Research Ethics of Inner Mongolia Agricultural University [Approval No. (2020) 056]. No specific permissions were required for these activities, and no endangered or protected species were involved. These activities were performed under the informed consent from all owners. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Difference in the growth stage of Zhongwei goat
Fig. 2
Fig. 2
(A) Analysis pipeline and descriptive statistics of phenotypes. Individuals were missed or supplemented during the two body size data collection periods, and we only used the 240 individuals with intact body size data for subsequent analysis. (B) A heatmap of the correlation coefficient between any two of ten body conformation traits. (C) The physical location of SNPs in the chromosome. (D) Population structure identified by principal component analysis. (E) Relationships between individuals
Fig. 3
Fig. 3
Manhattan plots of body conformation traits at 40d and 6 m for Zhongwei goats
Fig. 4
Fig. 4
Candidate-gene enrichment analysis. (A) Gene ontology (GO) enrichment. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment
Fig. 5
Fig. 5
Results of KASP genotyping analysis of 11 SNPs in Zhongwei goats. (A-K) Chr13_g.11,700,438 A > G, Chr15_g.37,120,328 A > G, Chr1_g.25,193,524 C > T, Chr6_g.7,209,383 C > T, Chr1_g.92,222,206 C > T, Chr20_g.51277932T > A, Chr19_g.17,078,199 A > G, Chr1_g.79,943,276 C > T, Chr14_g.7,618,442 A > G, Chr1_g.25,670,262 A > G, Chr21_g.16077504G > A, respectively. Genotyped samples marked red are wild type. Genotyped samples marked blue are homozygous mutant type. Genotyped samples marked green are heterozygous mutant type. Genotyped samples marked black are non template contrast
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