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Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks

文献类型： 外文期刊

作者： Xu, Tieshan 1 ; Xu, Zixin 1 ; Bai, Dingping 3 ; Wu, Fanghu 1 ; Shang, Yuanyuan 1 ; Li, Mao 1 ; Rong, Guang 1 ; Gu, Lihong 2 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Haikou 571100, Hainan, Peoples R China

2.Hainan Acad Agr Sci, Inst Anim Sci & Vet Med, Haikou 571101, Hainan, Peoples R China

3.Fujian Agr & Forestry Univ, Coll Anim Sci, Key Lab Tradit Chinese Vet Med & Anim Hlth Fujian, Fuzhou 350002, Fujian, Peoples R China

4.Henan Univ Sci & Technol, Coll Anim Sci, Luoyang 471900, Henan, Peoples R China

关键词： Jiaji ducks; SNP; cGPS liquid-phase microarray; GWAS; KASP

期刊名称：POULTRY SCIENCE （ 影响因子：4.2； 五年影响因子：4.5 ）

ISSN： 0032-5791

年卷期： 2025 年 104 卷 2 期

页码：

收录情况： SCI

摘要： 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 highquality 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.

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