Integration of Morphological and Genome-Wide SNP Data Reveals Regional Diversity in Thai Swamp Buffalo

Thai swamp buffalo (Bubalus bubalis) are valuable animal genetic resources, but their regional diversity remains incompletely characterized. Morphological records were obtained from 799 buffaloes, and 474 individuals were genotyped using the 90K Axiom® Buffalo SNP Genotyping Array (Thermo Fisher Scientific, Applied Biosystems™, Santa Clara, CA, USA). Qualitative traits included coat color, horn shape, chevron pattern, and hair-whorl distribution, while quantitative characterization covered 30 body measurements. After excluding missing traits, 30 traits adjusted for sex, age, province, and farm from 768 animals were used for morphology-based analyses, which identified regional phenotypic differences but also substantial overlap, consistent with the influence of feeding, management, environment, and local selection on body conformation. Genome-wide SNP analyses indicated a broadly shared genetic background with detectable regional structure, and runs of homozygosity revealed regional differences in genomic autozygosity. The Lower South showed a comparatively strong recurrent-ROH pattern, whereas inference for the Upper South requires caution because of its small genomic sample. Overall, integrating morphology and genome-wide SNP data improves regional characterization, but data-dependent statistics, population-structure estimates, and conservation implications should be interpreted while regarding small sampling and unbalanced data.