Genome wide identification of copy number variations cnvs and selective sweeps for production and adaptability traits in bos indicus cattle of TAMIL NADU

Abstract

Characterization of cattle genome to unravel the genetic mechanisms underlying phenotypic variations influenced by the environment and adaptations to distinct ecosystems shaped by natural selection is of utmost imperative. Therefore, the objective of this study is to describe the main effects of adaptation and selection in indicine cattle breeds of Tamil Nadu through the identification of copy number variants and selective sweep regions using whole-genome sequencing data. To achieve these objectives, whole genome sequencing was done using Illumina NovaSeqTM6000 and Illumina HiSeq 2500 for 15 pooled samples belonging to 79 animals of five cattle breeds of Tamil Nadu viz. Alambadi (14), Bargur (19), Kangayam (16), Pulikulam (16) and Umblachery (14) that were grouped as bulls, medium yielders and low yielders from each breed. Enriched terms associated with the emotional and behavioural control were described for the adaptive biological type, while those linked to the immune system as well as with reproductive and productive functions were for the productive biological type. In addition, four SNPs detected by whole genome sequencing in BTN1A1, MYO9B, MEGF11 and SSH2 genes were validated using tetra-primer ARMS-PCR and allele-specific PCR. Of these, genotypes pertaining to MYO9B and SSH2 genes were associated with milk production traits and somatic cell score respectively. newline Our findings improve the knowledge about the genome biology of cattle breeds of Tamil Nadu and provide candidate genes and genomic regions encompassing relevant traits as well as useful information for future conservation, association and selection approaches. newline newlineKey-words: Whole genome sequencing, Bos indicus, Pooled samples, Copy number variation regions, Signatures of selection, Production and adaptability traits. newline newline