biostudies-literatureJiao Yfengyang wang2702https://www.ebi.ac.uk/biostudies/studies/S-EPMC12466515biostudies-literatureUnknown15(18)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 validatiAnimals : an open access journal from MDPIDevelopment of a 5K Liquid-Phase Genome-Wide Breeding Chip for Xinglong Buffalo.PMC12466515[2025]100Jiang JChen QCui KWang FGao HLi LQiu XLi SMan CLi BChen SJiao YDu LChen TfalseDevelopment 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 validati2025-01-01T00:00:00Z2025 Sep2026-05-02T03:18:45.492Z2026-05-02T03:11:49.667ZS-EPMC124665154100794710.3390/ani15182702