Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken
Wenchang chicken is a native meat-type chicken breed in Hainan Province, China, known for its tender meat, which is in high demand both domestically and internationally. Improving important economic traits in Wenchang chicken is of significant importance to the poultry market. In this study, we geno...
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Elsevier
2025-05-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124013117 |
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| author | Ranran Zhu Yu Zhang Yuxiang Jiang Zihan Xu Yurong Tai Ziyi Lian Zhandeng Li Xiuping Wang Na Luo Guiping Zhao Xuemei Deng |
| author_facet | Ranran Zhu Yu Zhang Yuxiang Jiang Zihan Xu Yurong Tai Ziyi Lian Zhandeng Li Xiuping Wang Na Luo Guiping Zhao Xuemei Deng |
| author_sort | Ranran Zhu |
| collection | DOAJ |
| description | Wenchang chicken is a native meat-type chicken breed in Hainan Province, China, known for its tender meat, which is in high demand both domestically and internationally. Improving important economic traits in Wenchang chicken is of significant importance to the poultry market. In this study, we genotyped 3737 individuals from two generations of Hainan Wenchang chicken using the Jingxin No. 1 55K SNP chip, and subsequently imputed the chip data. After quality control, 41,086 high-quality SNPs were obtained. We performed weighted single-step genome-wide association study (wssGWAS) on six traits using a single-trait model, and searched for candidate genes within QTL regions explaining more than 1 % of the genetic variance. Based on the contribution to genetic variation from QTL regions, we identified 4, 8, 5, 6, 9, and 8 candidate regions for EP, 35w-EW, BW, FT, SL, and AFE, respectively. The top three significant windows cumulatively explained 5.03 %, 5.18 %, 19.05 %, 5.87 %, 6.15 %, and 3.86 % of the genetic variation for these traits, respectively. Within these regions, we identified 14 genes, including LDB2 and GIT1, which had previously been reported to be associated with ovarian development, body weight, and fat differentiation. The biological processes and pathways involving these genes include cartilage development, lipid molecule synthesis and metabolism, angiogenesis, and cell proliferation and migration. LDB2 was proposed as a strong candidate gene due to its significant function and high consistency with other studies regarding various carcass traits in chickens. Our findings provide valuable information for broiler breeding based on molecular selection. |
| format | Article |
| id | doaj-art-75d68db40d394de08117ac7e79f097b7 |
| institution | OA Journals |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-75d68db40d394de08117ac7e79f097b72025-08-20T01:51:42ZengElsevierPoultry Science0032-57912025-05-01104510473310.1016/j.psj.2024.104733Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chickenRanran Zhu0Yu Zhang1Yuxiang Jiang2Zihan Xu3Yurong Tai4Ziyi Lian5Zhandeng Li6Xiuping Wang7Na Luo8Guiping Zhao9Xuemei Deng10Sanya Institute, China Agricultural University, Sanya 572025, China; State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement and Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaSanya Institute, China Agricultural University, Sanya 572025, China; State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement and Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaSanya Institute, China Agricultural University, Sanya 572025, China; State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement and Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaSanya Institute, China Agricultural University, Sanya 572025, ChinaSanya Institute, China Agricultural University, Sanya 572025, China; Hainan Seed Industry Laboratory, Yazhou 572024, ChinaSanya Institute, China Agricultural University, Sanya 572025, China; State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement and Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaHainan (Tan Niu) Wenchang Chicken Co., LTD, Haikou 570100, ChinaHainan (Tan Niu) Wenchang Chicken Co., LTD, Haikou 570100, ChinaChinese Academy of Agricultural Sciences, Beijing, 100193 ChinaChinese Academy of Agricultural Sciences, Beijing, 100193 ChinaSanya Institute, China Agricultural University, Sanya 572025, China; State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement and Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Corresponding author at: Sanya Institute, China Agricultural University, Sanya 572025, China.Wenchang chicken is a native meat-type chicken breed in Hainan Province, China, known for its tender meat, which is in high demand both domestically and internationally. Improving important economic traits in Wenchang chicken is of significant importance to the poultry market. In this study, we genotyped 3737 individuals from two generations of Hainan Wenchang chicken using the Jingxin No. 1 55K SNP chip, and subsequently imputed the chip data. After quality control, 41,086 high-quality SNPs were obtained. We performed weighted single-step genome-wide association study (wssGWAS) on six traits using a single-trait model, and searched for candidate genes within QTL regions explaining more than 1 % of the genetic variance. Based on the contribution to genetic variation from QTL regions, we identified 4, 8, 5, 6, 9, and 8 candidate regions for EP, 35w-EW, BW, FT, SL, and AFE, respectively. The top three significant windows cumulatively explained 5.03 %, 5.18 %, 19.05 %, 5.87 %, 6.15 %, and 3.86 % of the genetic variation for these traits, respectively. Within these regions, we identified 14 genes, including LDB2 and GIT1, which had previously been reported to be associated with ovarian development, body weight, and fat differentiation. The biological processes and pathways involving these genes include cartilage development, lipid molecule synthesis and metabolism, angiogenesis, and cell proliferation and migration. LDB2 was proposed as a strong candidate gene due to its significant function and high consistency with other studies regarding various carcass traits in chickens. Our findings provide valuable information for broiler breeding based on molecular selection.http://www.sciencedirect.com/science/article/pii/S0032579124013117Wenchang chickenwssGWASEconomic traitsCandidate genes |
| spellingShingle | Ranran Zhu Yu Zhang Yuxiang Jiang Zihan Xu Yurong Tai Ziyi Lian Zhandeng Li Xiuping Wang Na Luo Guiping Zhao Xuemei Deng Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken Poultry Science Wenchang chicken wssGWAS Economic traits Candidate genes |
| title | Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken |
| title_full | Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken |
| title_fullStr | Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken |
| title_full_unstemmed | Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken |
| title_short | Weighted single-step genome-wide association study identified genomic regions and candidate genes for growth and reproductive traits in Wenchang chicken |
| title_sort | weighted single step genome wide association study identified genomic regions and candidate genes for growth and reproductive traits in wenchang chicken |
| topic | Wenchang chicken wssGWAS Economic traits Candidate genes |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124013117 |
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