From Genes to Pastures: Unraveling Ancestry, Admixture, and Environmental Adaptations of Beef Cattle in Hawai‘i

Abstract

Cattle ranching in Hawai‘i, shaped by its unique climate and geography, is of historical and contemporary significance. Yet comprehensive genomic studies of Hawaiian cattle remain scarce. This is the first dedicated genomic study of Hawaiian cattle, which decoded the genetic background, breed composition, and genetic variants governing cattle production and climate adaptation.In this study, we collected blood samples from 351 cattle heads spanning 11 ranches across four Hawaiian islands and genotyped them with Neogen GGP 100K SNP chips. Genetic admixture and divergence events in the Hawaiian cattle population were analyzed to decode cattle ancestry and deduce the evolution of cattle breeds on Hawaiian lands historically. These data were further used for two association studies, including the Genome-Wide Association Study (GWAS) and the Genome-Environment Association Study (GEA). In addition, we collected tissue samples from the digestive tract of pasture-finished cattle at the Mealani Research Station, belonging to the University of Hawai‘i at Mānoa. We performed a transcriptomics study to understand the roles of diet and the influence of production systems in health and immune defense mechanisms against biotic and abiotic stress. This study identified the dominance of Angus beef cattle in Hawai‘i. However, the present-day Hawaiian Angus was drifting away from their original lineage. Admixture and interactions among genetics, environments, and selection pressures may have significantly played roles in developing new breed entities in this isolated geography with diverse climates. We identified an admixture of one to ten percent of indicine lineage from the Brahman breed in continental Angus, which developed into a tropical Hawaiian Angus, as novel findings of this study. GWAS and GEA studies identified genetic variants and candidate genes, including RGS20, ZMAT3, RUVBL1, EEFEC, and SEC61A1, associated with production and adaptation in tropical pasture-based conditions. A comparative transcriptomics study of cattle subjected to grain-fed versus pasture-fed diets revealed diet-induced gastrointestinal dysfunctions. Cattle fed a more hygienic diet and raised in open pasture-based production showed promoted gut health and defense against stress. This was evidenced by upregulations of Mitogen-Activated Protein Kinases (MAPKs) and downregulations of proinflammatory cytokines. This study opens a door for future genomic studies in the Hawaiian beef cattle population, exploring their unique traits and quality, particularly in comparative studies with cohorts from Hawaiian Angus adapted to tropical environments, can be valuable genetic resources for crossbreeding as a strategy for combating observed consequences of climate change.