Development of a 5K Liquid-Phase Genome-Wide Breeding Chip for Xinglong Buffalo

Area of Science:

• Animal Genetics
• Genomics
• Molecular Breeding

Background:

• The Xinglong buffalo is a vital indigenous swamp buffalo breed in China.
• Effective conservation and utilization of its genetic resources are crucial.

Purpose of the Study:

• To develop a breed-specific single nucleotide polymorphism (SNP) liquid-phase chip for Xinglong buffalo.
• To support molecular breeding, conservation, and genetic evaluation.

Main Methods:

• Genotyping-by-target-sequencing (GBTS) technology was used.
• Whole-genome resequencing data from 143 buffaloes identified breed-specific, background, and functional SNPs.
• A 5K liquid-phase genome-wide breeding chip was developed and validated.

Main Results:

• A 5K SNP chip comprising 5062 sites was successfully developed for Xinglong buffalo.
• The chip demonstrated high detection rates, repeatability, and consistency in validation.
• The chip proved effective for clustering and kinship analysis, highlighting breed specificity.

Conclusions:

• The developed SNP chip is a low-density, cost-effective tool for accurate Xinglong buffalo genotyping.
• This resource will advance molecular breeding, conservation, and genetic evaluation efforts.
• It facilitates the sustainable utilization of this valuable indigenous germplasm.