Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

SIMPLE SUMMARY: Abigar cattle, native to southwestern Ethiopia’s hot and humid environment, are recognized for their adaptability and vital contribution to local livelihoods and the livestock value chain. Investigating their genetic basis for adaptive traits is crucial for sustainable use. However, there is a paucity of studies on genomic diversity, population structure, and selection signatures of Abigar cattle. This study introduces the first whole-genome sequencing of Abigar cattle, revealing genes linked to heat tolerance, immune response, and stress resilience in tropical conditions. These findings offer essential genomic insights for future Abigar cattle breeding. ABSTRACT: Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (F(ST)) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.