Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Indigenous cattle breeds (Bos indicus) inhabited under diverse agroclimatic conditions may serve as a broad reservoir of genetic pool for identifying genes selected for local adaptation. The present study aimed at deciphering genomic diversity and identifying adaptation signatures of cattle breeds belonging to contrasting agro-climatic conditions: Siri and Ladakhi from cold hilly region; and Kankrej and Hallikar from hot arid and semi-arid regions, respectively. A total of 46 samples were genotyped using 777 K Illumina BovineHD BeadChip. The Principal Component Analysis brought together Hallikar and Kankrej, while Siri and Ladakhi formed a separate cluster. In contrast to the tropical cattle breeds, genetic variation was higher for temperate type. Linkage disequilibrium decay (r² < 0.2) in hot semi-arid/arid adapted (71–103 kb) and temperate-adapted (218–222 kb) breeds revealed that BovineHD BeadChip can be used in predicting their genomic breeding values. Runs of homozygosity and F_ST based selection signatures were also identified in these cattle breeds. Novel hypoxia-related genes viz. egl-9 family hypoxia inducible factor, hypoxia inducible factor 1 subunit alpha inhibitor and heme oxygenase 1 were detected in temperate adapted breeds, while heat stress (heat shock protein family H (Hsp110) member 1 and BAG cochaperone 2 and immunity (TANK binding kinase 1) related genes were identified in selection sweeps of tropical breeds. Gene ontology analysis identified several enriched terms for the genes in both hot semi-arid/arid and temperate adapted cattle breeds in ROH islands. The relevant adaptation signals found in the present study will help to establish new breeding opportunities with recognition of core genes.