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

## TL;DR

This study explores the genetic origins and adaptations of native cattle in the Visayas region of the Philippines, revealing their indicine ancestry and traits suited to tropical island conditions.

## Contribution

The study identifies genomic regions linked to local adaptation in Visayan native cattle, offering insights into their ancestry and traits for conservation and breeding.

## Key findings

- Visayan native cattle show indicine ancestry bridging mainland Southeast Asia and China with additional taurine and South Asian indicine components.
- Candidate genes suggest adaptations for small stature, heat tolerance, and reproductive performance in tropical island environments.
- Low genetic diversity and long ROH segments in Siquijor cattle indicate recent inbreeding.

## Abstract

Philippine farmers utilize native cattle for meat, draft power, and income security, but until now their origins and perceived traits have been poorly understood. This study utilized genome-wide SNP to analyze native cattle from the Panay and Siquijor islands, Visayas, comparing them to global breeds to uncover their origin and the genomic regions that potentially allow them to thrive in a tropical island environment. Visayan native cattle mostly belonged to indicine cattle and occupied a middle position between mainland Southeast Asian and Southern Chinese cattle, reflecting past mixing among these regions. Their genetic history is consistent with a complex sequence of ancestry signals that may reflect historical livestock movements associated with Southeast Asian maritime connectivity and later colonial-era introductions. Finally, several candidate regions were identified, and these could be related to the traits perceived by local farmers.

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.