Xu Tieshan, Xu Zixin, Bai Dingping, Wu Fanghu, Shang Yuanyuan, Li Mao, Rong Guang, Gu Lihong
Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, Haikou 571100, PR China.
Tropical 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 China.
Poult Sci. 2025 Feb;104(2):104737. doi: 10.1016/j.psj.2024.104737. Epub 2024 Dec 24.
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.
为了为家系鸭的分子育种提供一种低成本、高效且高精度的工具，我们首次利用这一珍贵家禽品种的重测序数据构建了一个cGPS（捕获目标精准测序基因分型）20K液相微阵列。该微阵列包含20327个高质量单核苷酸多态性（SNP）位点，主要来自本研究收集的30个家系鸭重测序样本，部分位点从中国科学院昆明动物研究所的135个鸭重测序数据中补充。该微阵列在两次生产测试中表现出优异性能。利用该微阵列对236只家系鸭群体进行基因分型，然后将基因分型数据用于群体结构分析和羽色表型的全基因组关联研究（GWAS）。根据群体结构分析，利用遗传距离矩阵可将家系鸭群体分为四个亚群。通过GWAS分析，在14号染色体上一个包含30个基因的区域内鉴定出38个显著的SNP位点。其中，EDNRB2和VAMP7被确定为家系鸭羽色调控的强候选基因。EDNRB2上游的两个突变被确定与无色表型紧密连锁。此外，针对与EDNRB2相关的SNP位点（HIC_SCAFFOLD_14_14984620，HIC_SCAFFOLD_14_15016766）设计了两个竞争性等位基因特异性PCR（KASP）标记。KASP基因分型结果显示，SNP位点HIC_SCAFFOLD_14_15016766上不同基因型与羽色表型之间存在强相关性。总之，这种自主设计的微阵列将有助于大规模基因分型，并可为未来突变位点和功能基因的筛选奠定基础。
