Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat
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...
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11097-1 |
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| author | Mingxuan Han Xinbo Wang Haidong Du Yanlong Cao Zhanqiang Zhao Shuran Niu Xuxu Bao Youjun Rong Xiaofang Ao Furong Guo Qincheng Xia Fangzheng Shang Ruijun Wang Yanjun Zhang |
| author_facet | Mingxuan Han Xinbo Wang Haidong Du Yanlong Cao Zhanqiang Zhao Shuran Niu Xuxu Bao Youjun Rong Xiaofang Ao Furong Guo Qincheng Xia Fangzheng Shang Ruijun Wang Yanjun Zhang |
| author_sort | Mingxuan Han |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e3b63e25f07246678f76d64d29a41e48 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-e3b63e25f07246678f76d64d29a41e482025-01-19T12:11:26ZengBMCBMC Genomics1471-21642025-01-0126111510.1186/s12864-024-11097-1Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goatMingxuan Han0Xinbo Wang1Haidong Du2Yanlong Cao3Zhanqiang Zhao4Shuran Niu5Xuxu Bao6Youjun Rong7Xiaofang Ao8Furong Guo9Qincheng Xia10Fangzheng Shang11Ruijun Wang12Yanjun Zhang13College of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityZhongwei Goat Breeding FarmZhongwei Goat Breeding FarmZhongwei Goat Breeding FarmCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityAbstract 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.https://doi.org/10.1186/s12864-024-11097-1Zhongwei goatRe-sequenceBody conformation traitsGWASKASP validation |
| spellingShingle | Mingxuan Han Xinbo Wang Haidong Du Yanlong Cao Zhanqiang Zhao Shuran Niu Xuxu Bao Youjun Rong Xiaofang Ao Furong Guo Qincheng Xia Fangzheng Shang Ruijun Wang Yanjun Zhang Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat BMC Genomics Zhongwei goat Re-sequence Body conformation traits GWAS KASP validation |
| title | Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat |
| title_full | Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat |
| title_fullStr | Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat |
| title_full_unstemmed | Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat |
| title_short | Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat |
| title_sort | genome wide association study identifies candidate genes affecting body conformation traits of zhongwei goat |
| topic | Zhongwei goat Re-sequence Body conformation traits GWAS KASP validation |
| url | https://doi.org/10.1186/s12864-024-11097-1 |
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