Development and Characterization of a 100 K SNP Panel Through Genotyping by Target Sequencing in Asian Water Buffalo ( Bubalus bubalis )

ABSTRACT High‐throughput and cost‐effective genotyping technologies are essential for animal genomics and breeding research. In this study, we developed a 100 K single nucleotide polymorphism (SNP) panel for genomic screening of Asian water buffalo using genotyping by target sequencing (GBTS). The panel consists of 101 032 SNPs, selected to include highly polymorphic variants from an existing SNP array—the Axiom 90 K Genotyping Array (16.6%), moderate‐ to high‐impact variants in protein‐coding genes (20.3%), swamp‐ and river‐specific variants (10.6%), variants in functional genes associated with economic traits (0.9%), variants located on the X chromosome (0.6%) as well as gap‐filling variants (51.0%). To validate the panel, we genotyped 78 buffaloes using the panel as well as whole‐genome sequencing (WGS). The panel achieved an average call rate of 99.77%, with a mean genotype concordance of 99.43% across five replicate samples. Population genomics analyses using the panel yielded results highly consistent with those obtained from WGS. When using WGS data as the reference panel, the 100 K SNP panel achieved high imputation accuracy across three buffalo populations—0.89 in dairy river, 0.84 in local river, and 0.81 in swamp buffalo. After applying a stringent quality‐control filter (D R 2 > 0.9), the retained variants exhibited mean imputation accuracy > 0.90 in all populations while preserving a substantial number of high‐quality SNPs (10.40, 5.59, and 2.50 million SNPs, respectively). Overall, the newly designed 100 K SNP panel represents a robust, high‐throughput tool for genome‐wide genotyping, facilitating the conservation of genetic resources and enabling sustainable genetic improvement of water buffalo populations.