Research note: A low-density SNP genotyping panel for Chinese native chickens

Area of Science:

• Animal Genetics
• Genomics
• Molecular Breeding

Background:

• Genotyping costs are a major limitation in molecular breeding and population genetic studies for poultry.
• Poultry's smaller genome and lower individual value necessitate cost-effective genotyping solutions compared to livestock like cattle and sheep.

Purpose of the Study:

• To develop a low-density single nucleotide polymorphism (SNP) genotyping panel for chickens to reduce costs.
• To evaluate the panel's efficacy in population genetic analyses and genomic prediction.

Main Methods:

• Developed an 11K SNP genotyping panel using genotyping by targeted sequencing (GBTS).
• Designed the panel based on whole genome sequencing data from eight chicken breeds (7 local, 1 commercial).
• Applied the panel to population structure analysis and genomic prediction in Wenshang Barred chickens.

Main Results:

• The 11K SNP panel demonstrated high SNP call rates and minor allele frequencies (MAF), enabling clear population and family differentiation.
• Genomic prediction using the 11K panel showed comparable predictive ability and accuracy to whole genome sequencing (WGS) data.
• The panel proved efficient and cost-effective for genetic analysis in local Chinese chickens.

Conclusions:

• The developed 11K SNP panel is a cost-effective and efficient tool for chicken breeding and genetic analysis.
• This low-density panel can accelerate genetic improvements and support conservation initiatives for local chicken breeds.
• The findings support the broader application of SNP genotyping in poultry research and breeding programs.