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

The Xinglong buffalo is a local swamp buffalo breed adapted to tropical regions in China. To facilitate the protection and utilization of valuable genetic resources, we first developed the breed-specific single nucleotide polymorphism (SNP) liquid-phase chip based on genotyping-by-target-sequencing (GBTS) technology. Whole-genome resequencing data from 143 buffaloes, resulting in 34,757,694 SNPs, were used to identify 1208 breed-specific and 2889 background sites. This chip also incorporates 965 functional SNP sites derived from literature, including SNPs significantly associated with immunity, reproduction, growth, and production. A total of 5062 SNP sites were successfully identified for the development of a 5K liquid-phase genome-wide breeding chip for the Xinglong buffalo. The validation of the chip using 93 samples showed a high detection rate with good repeatability and consistency. In addition, the chip exhibits strong capabilities in clustering and kinship analysis. Results of kinship analysis underscored the importance of a breed-specific chip for the Xinglong buffalo. These results highlight the advantages of a low-density, cost-effective, and breed-specific SNP chip for accurate genotyping. This chip will support future endeavors in molecular breeding, conservation, and genetic evaluation of Xinglong buffalo, thereby facilitating the sustainable utilization of this valuable indigenous germplasm resource.