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

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 f...

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Bibliographic Details
Published in:3 Biotech 2023-03, Vol.13 (3), p.86-86, Article 86
Main Authors: Bhardwaj, Shivam, Singh, Sanjeev, Ganguly, Indrajit, Bhatia, Avnish Kumar, Dixit, S. P.
Format: Article
Language:English
Subjects:
Adaptation
Agriculture
Amino acid sequence
Amino acids
Bioinformatics
Biomaterials
Biotechnology
Bos taurus indicus
Cancer Research
Cattle
Chemistry
Chemistry and Materials Science
Climatic conditions
Collinearity
Environmental conditions
Genes
Genomics
Genotypes
Mutants
Original
Original Article
Protein structure
Proteins
Quality control
Single-nucleotide polymorphism
Stem Cells
Structure-function relationships
USP18 protein
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Summary: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  
ISSN:2190-572X
2190-5738
DOI:10.1007/s13205-023-03493-3