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


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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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Submitted

2023-05-09

Published

2023-08-31

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How to Cite

SHARMA, N. K., SINGH, P., SAHA, B., BHARDWAJ, A., IQUEBAL, M. A., PAL, Y., NAYAN, V., JAISWAL, S., GIRI, S. K., LEGHA, R. A., BHATTACHARYA, T. K., KUMAR, D., RAI, A., & TRIPATHI, B. N. (2023). Genome-wide copy number variations in Bhutia equine breed using SNP genotyping data. The Indian Journal of Animal Sciences, 93(8), 802–805. https://doi.org/10.56093/ijans.v93i8.136161
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