Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks
In order to provide a low-cost, high efficient, and highly accurate tool for molecular breeding of Jiaji ducks, we constructed a cGPS(Genotyping by Pinpoint Sequencing of captured targets) 20 K liquid-phase microarray using resequencing data from this valuable poultry breed for the first time. The m...
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Elsevier
2025-02-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124013154 |
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| author | Tieshan Xu Zixin Xu Dingping Bai Fanghu Wu Yuanyuan Shang Mao Li Guang Rong Lihong Gu |
| author_facet | Tieshan Xu Zixin Xu Dingping Bai Fanghu Wu Yuanyuan Shang Mao Li Guang Rong Lihong Gu |
| author_sort | Tieshan Xu |
| collection | DOAJ |
| description | In order to provide a low-cost, high efficient, and highly accurate tool for molecular breeding of Jiaji ducks, we constructed a cGPS(Genotyping by Pinpoint Sequencing of captured targets) 20 K liquid-phase microarray using resequencing data from this valuable poultry breed for the first time. The microarray contains 20,327 high-quality snp loci, mainly from the 30 Jiaji duck resequencing samples collected in this study, and some loci were supplemented from the 135 duck resequencing data from KUNMING INSTITUTE OF ZOOLOGY.CAS. This microarray showed excellent performance in two production tests. The microarray was used to genotype a population of 236 Jiaji ducks, and the genotyping data were then used for population structure analysis and genome-wide association studies (GWAS) of plumage color phenotypes. According to the population structure analysis, the population of Jiaji ducks could be divided into four subpopulations using genetic distance matrices. Using GWAS analysis, 38 significant SNP loci were identified within a region on chromosome 14 that contained 30 genes. Among them, EDNRB2 and VAMP7 were identified as strong candidate genes for the regulation of plumage color in Jiaji ducks. Two mutations upstream of EDNRB2 were identified as tightly linked to the colorless phenotype. In addition, two KASP markers were designed for the SNP loci associated with EDNRB2 (HIC_SCAFFOLD_14_14984620, HIC_SCAFFOLD_14_15016766). The KASP genotyping results showed strong correlations between different genotypes on the SNP locus HIC_SCAFFOLD_14_15016766 and the plumage phenotype. In conclusion, this independently designed microarray will be useful for large-scale genotyping and can lay the foundation for future screening of mutation loci and functional genes. |
| format | Article |
| id | doaj-art-58d50584a4864d0b8ecf34f92aa8d6c3 |
| institution | OA Journals |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-58d50584a4864d0b8ecf34f92aa8d6c32025-08-20T02:01:24ZengElsevierPoultry Science0032-57912025-02-01104210473710.1016/j.psj.2024.104737Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducksTieshan Xu0Zixin Xu1Dingping Bai2Fanghu Wu3Yuanyuan Shang4Mao Li5Guang Rong6Lihong Gu7Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR China; Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, PR ChinaKey Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, PR ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR China; College of Animal Science, Henan University of Science and Technology, Henan, Luoyang 471900, PR ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR China; College of Animal Science, Henan University of Science and Technology, Henan, Luoyang 471900, PR ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR ChinaInstitute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Hainan, Haikou 571101, PR China; Corresponding author at: Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Hainan, Haikou 571100, PR China.In order to provide a low-cost, high efficient, and highly accurate tool for molecular breeding of Jiaji ducks, we constructed a cGPS(Genotyping by Pinpoint Sequencing of captured targets) 20 K liquid-phase microarray using resequencing data from this valuable poultry breed for the first time. The microarray contains 20,327 high-quality snp loci, mainly from the 30 Jiaji duck resequencing samples collected in this study, and some loci were supplemented from the 135 duck resequencing data from KUNMING INSTITUTE OF ZOOLOGY.CAS. This microarray showed excellent performance in two production tests. The microarray was used to genotype a population of 236 Jiaji ducks, and the genotyping data were then used for population structure analysis and genome-wide association studies (GWAS) of plumage color phenotypes. According to the population structure analysis, the population of Jiaji ducks could be divided into four subpopulations using genetic distance matrices. Using GWAS analysis, 38 significant SNP loci were identified within a region on chromosome 14 that contained 30 genes. Among them, EDNRB2 and VAMP7 were identified as strong candidate genes for the regulation of plumage color in Jiaji ducks. Two mutations upstream of EDNRB2 were identified as tightly linked to the colorless phenotype. In addition, two KASP markers were designed for the SNP loci associated with EDNRB2 (HIC_SCAFFOLD_14_14984620, HIC_SCAFFOLD_14_15016766). The KASP genotyping results showed strong correlations between different genotypes on the SNP locus HIC_SCAFFOLD_14_15016766 and the plumage phenotype. In conclusion, this independently designed microarray will be useful for large-scale genotyping and can lay the foundation for future screening of mutation loci and functional genes.http://www.sciencedirect.com/science/article/pii/S0032579124013154Jiaji ducksSNPcGPS liquid-phase microarrayGWASKASP |
| spellingShingle | Tieshan Xu Zixin Xu Dingping Bai Fanghu Wu Yuanyuan Shang Mao Li Guang Rong Lihong Gu Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks Poultry Science Jiaji ducks SNP cGPS liquid-phase microarray GWAS KASP |
| title | Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks |
| title_full | Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks |
| title_fullStr | Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks |
| title_full_unstemmed | Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks |
| title_short | Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks |
| title_sort | development and application of a cgps 20k liquid phase snp microarray in jiaji ducks |
| topic | Jiaji ducks SNP cGPS liquid-phase microarray GWAS KASP |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124013154 |
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