GENETIC DIFFERENTIATION OF SWAMP BUFFALOES IN CALAYAN AND TAWI-TAWI USING 90K SNP GENOTYPING PANEL FOR INCLUSIVE BREEDING CONSERVATION

Pauleen S. Pineda, Maureen B. Gajeton, Sherwin D. Matias, Ester B. Flores

Abstract


Water buffaloes are a significant livestock resource that helps rural farmers by providing draft power, milk, meat, and hides. However, crossbreeding between the two water buffalo types—swamp and river—has raised concerns about preserving the genetic identity of native swamp populations. In this study, 58 water buffaloes from an institutional swamp herd, Tawi-Tawi, Calayan Islands, and crossbreds were genotyped using a 90K single-nucleotide polymorphism (SNP) buffalo genotyping panel. A total of 54,481 polymorphic SNPs were used after filtering. The mean fixation index (FST) is 0.37, indicating substantial genetic differentiation between swamp populations. A high-impact SNP predicted to disrupt gene function was identified in ADCY2, a gene previously linked to meat quality traits. Additionally, 148 SNPs were shared exclusively among swamp buffalo groups and absent in crossbreds, highlighting potential markers specific to swamp buffalo that may help in breed traceability.  Principal Component Analysis (PCA) revealed distinct clustering among swamp populations, particularly between those from Calayan and Tawi-Tawi. However, the panel’s applicability to swamp buffaloes is limited, as only 36% SNPs had a minor allele frequency (MAF) > 0.05. Nevertheless, the SNP data effectively revealed population structure among swamp and crossbred buffaloes, offering valuable insights for conservation and breeding strategies.

Keywords


animal breeding, genetic conservation, genotyping, SNPs, variations

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References


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