Designing and evaluating a cost-effective single nucleotide polymorphism liquid array for Chinese native chickens

Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid-phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high-quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome-wide association study of broilers, resulting in the identification of several growth- and meat quality-related loci. Therefore, the newly developed chip is efficient, cost-effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.