Genome-wide copy number variations in Bhutia equine breed using SNP genotyping data

NITESH KUMAR SHARMA; PRASHANT SINGH; BIBEK SAHA; ANURADHA BHARDWAJ; MIR ASIF IQUEBAL; YASH PAL; VARIJ NAYAN; SARIKA JAISWAL; SHIV KUMAR GIRI; RAM AVATAR LEGHA; T K BHATTACHARYA; DINESH KUMAR; ANIL RAI; BHUPENDRA NATH TRIPATHI

doi:10.56093/ijans.v93i8.136161

Authors

NITESH KUMAR SHARMA ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
PRASHANT SINGH ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana
BIBEK SAHA ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
ANURADHA BHARDWAJ ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana
MIR ASIF IQUEBAL ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
YASH PAL ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana
VARIJ NAYAN ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana
SARIKA JAISWAL ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
SHIV KUMAR GIRI Maharaja Agrasen University, Baddi, Himachal Pradesh
RAM AVATAR LEGHA ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana
T K BHATTACHARYA ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana
DINESH KUMAR ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
ANIL RAI ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110 012 India
BHUPENDRA NATH TRIPATHI ICAR, New Delhi

https://doi.org/10.56093/ijans.v93i8.136161

Keywords:

Bhutia, Copy number variation (CNV), Copy number variation region (CNVR), Equine, Genes

Abstract

Copy number variants (CNVs) have dynamic potential and evolutionary significance like other genetic variants, namely, single nucleotide polymorphisms, InDels, short tandem repeat polymorphisms, inversion variants, etc. Discovering CNVs leads to further speculation that the genomic DNA contains more changes than previously thought and contributes to the phenotypic variation. CNVs are big DNA fragments (> 1 kb) being duplicated or deleted. A bridge between CNVs and phenotypic variations supports CNVs to be utilized in GWAS, which are currently mostly based on SNPs. CNV, which refers to the structural differences, influence gene expression and can be an indicator of numerous traits for improvement. There is a severe dearth of research on CNVs in animals, especially equine. The present study investigates the genomes of the Bhutia Equine breed for genome-wide discovery of CNVs using the
Axiom™ Equine Genotyping Array chip for a better understanding of its traits which had been unexplored till date. A total of 619 CNVs from 20 Bhutia equines were identified with the median and average size as 49.394 kb and 114.955 kb, respectively. Total 225 frequent CNVRs with > 1% CNV frequency were identified among them along with singleton type. These CNVRs contained 361 genes in all. The information obtained on genomic variation could be utilized to identify economically advantageous genetic features in Bhutia equine breed.

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