Deciphering local adaptation of native Indian cattle (<i>Bos indicus</i>) breeds using landscape genomics and in-silico prediction of deleterious SNP effects on protein structure and function.

ABSTRACT: India has 50 registered breeds of native cattle (Bos indicus) which are locally adapted to diverse environmental conditions. This study aimed to investigate the genomic basis of adaptation of native Indian cattle and to predict the impact of key SNPs on the amino acid changes that affect protein function. The Illumina 777 K BovineHD BeadChip was used to genotype 178 native cattle belonging to contrasting landscapes and agro-climatic conditions. The genotype-environment association was investigated with R. SamBada, using 5,74,382 QC passed SNPs and 11 predictor variables (10 multi-collinearity controlled environmental variables and 1 variable as "score of PCA" on ancestry coefficients of individuals). In total, 1,12,780 models were selected as significant (q < 0.05) based on <

SUBMITTER: Bhardwaj S 

PROVIDER: S-EPMC9931982 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature