Performance of Illumina® BovineHD BeadChip in genotyping Indian riverine buffalo breeds


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Authors

  • HEENA SHAH National Dairy Development Board, Anand, Gujarat 388 001 India
  • A SUDHAKAR National Dairy Development Board, Anand, Gujarat 388 001 India
  • SANDEEP KUMAR DONTHULA National Dairy Development Board, Anand, Gujarat 388 001 India
  • HARDIK POOJARA National Dairy Development Board, Anand, Gujarat 388 001 India
  • SWAPNIL GAJJAR National Dairy Development Board, Anand, Gujarat 388 001 India
  • SUJIT SAHA National Dairy Development Board, Anand, Gujarat 388 001 India
  • NILESH NAYEE National Dairy Development Board, Anand, Gujarat 388 001 India

https://doi.org/10.56093/ijans.v92i10.121632

Keywords:

Buffalo, BovineHD, Genotyping, Polymorphic, SNP

Abstract

The current study tested the suitability of Illumina® BovineHD BeadChip in genotyping three riverine breeds of buffalo viz. Jaffarabadi, Murrah and Mehsana. Of the 777962 SNPs, 670955 SNPs were called in all animals and only 13150 SNPs were found to be polymorphic at a call rate of 90%, and had Minor Allele Frequency (MAF) greater than 0.05. The average Minor Allele Frequency (MAF) of polymorphic SNPs was 0.23 and average expected heterozygosity (HE) of 0.321. Principal Component Analysis (PCA) revealed 2 different clusters where Murrah and Mehsana breeds clustered together, while Jaffarabadi breed formed a distinct cluster. Result obtained in this study indicated that the SNPs available in Illumina BovineHD BeadChip may not be good enough for studying population structure and genetic analyses in Indian buffalo breeds. Hence it might be necessary to develop a custom SNP marker panel for Indian riverine buffaloes.

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Submitted

2022-07-17

Published

2022-10-11

Issue

Vol. 92 No. 10 (2022)

Section

Short-Communication

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The copyright of the articles published in The Indian Journal of Animal Sciences is vested with the Indian Council of Agricultural Research, which reserves the right to enter into any agreement with any organization in India or abroad, for reprography, photocopying, storage and dissemination of information. The Council has no objection to using the material, provided the information is not being utilized for commercial purposes and wherever the information is being used, proper credit is given to ICAR.

How to Cite

SHAH, H., SUDHAKAR, A., DONTHULA, S. K., POOJARA, H., GAJJAR, S., SAHA, S., & NAYEE, N. (2022). Performance of Illumina® BovineHD BeadChip in genotyping Indian riverine buffalo breeds. The Indian Journal of Animal Sciences, 92(10), 1179–1181. https://doi.org/10.56093/ijans.v92i10.121632
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