Genomic Insights into the Origins, Population Structure, and Local Adaptation of Philippine Visayan Native Cattle

The introduction of domestic cattle to the Philippines is often attributed to Spanish and Chinese sources, yet the origins and adaptive history of Philippine Visayan native cattle remain unclear. This study examined the ancestry, structure, and putative selection signals of the Visayan native cattle from Panay and Siquijor islands (VNC) in a global context. Using genome-wide SNP data, population structure was assessed by PCA, IBS/Nei/FST trees, and ADMIXTURE; historical relationships were explored with migration, f-statistics, and an admixture graph; and positive selection was scanned using commonly used methods such as ROH, Tajima’s D, iHS/XP-EHH, and FST with cross-validation across methods and functional enrichment of the overlapping regions. VNC exhibited low-to-moderate genetic diversity (Ho and He ≈ 0.21; and FIS = 0.01 to 0.02) with Siquijor enriched for long ROH segments indicating recent inbreeding. Across multiple complementary analyses, VNC showed predominantly indicine ancestry and occupied an intermediate bridge-like position between indicine from mainland Southeast Asia and from Southeastern China, with additional components that were most similar to Iberian taurine cattle and South Asian indicine. Moreover, the current study identified putative selection signatures that would possibly provide insights to better understand the local adaptation of VNC under insular tropical conditions of the Philippines: (1) small stature (HOXC cluster, STAC3, NXPH4, STARD13, RTN1), (2) heat tolerance and immune robustness (NDUFA4L2, SHMT2, ATP5MC2, ATF7, R3HDM2, CALCOCO1); (3) early reproductive and maturity reproductive performance (IGF2BP2, KL, LRP1, PDS5B). Overall, the VNC in Panay and Siquijor showed a predominantly indicine ancestry with putatively island-adapted physiology, emphasizing the need for conservation and island-specific breeding that preserves local adaptation while managing inbreeding.