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

Area of Science:

• Animal Genetics
• Genomics
• Molecular Breeding

Background:

• Jiaji ducks are a valuable poultry breed requiring efficient molecular breeding tools.
• Existing genotyping methods may lack the desired efficiency and accuracy for large-scale applications.

Purpose of the Study:

• To construct a cost-effective, high-efficiency, and accurate genotyping tool for Jiaji duck molecular breeding.
• To identify genetic loci and candidate genes associated with plumage color in Jiaji ducks.

Main Methods:

• Construction of a 20K liquid-phase microarray (cGPS) using resequencing data.
• Genotyping of 236 Jiaji ducks for population structure analysis and genome-wide association studies (GWAS).
• Development of KASP markers for identified SNP loci.

Main Results:

• The cGPS microarray demonstrated excellent performance in production tests.
• Population structure analysis revealed four subpopulations.
• GWAS identified 38 significant SNP loci on chromosome 14, implicating EDNRB2 and VAMP7 as candidate genes for plumage color.
• Mutations upstream of EDNRB2 were linked to the colorless phenotype, and KASP markers showed strong genotype-phenotype correlations.

Conclusions:

• The independently designed microarray is suitable for large-scale Jiaji duck genotyping.
• This tool provides a foundation for future screening of mutation loci and functional genes in Jiaji ducks.
• The identified genetic markers and candidate genes advance molecular breeding strategies for this breed.