Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds.

Abstract:

:In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r2 < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.

journal_name

Anim Biotechnol

journal_title

Animal biotechnology

authors

Dash S,Singh A,Bhatia AK,Jayakumar S,Sharma A,Singh S,Ganguly I,Dixit SP

doi

10.1080/10495398.2017.1329150

subject

Has Abstract

pub_date

2018-04-03 00:00:00

pages

129-135

issue

2

eissn

1049-5398

issn

1532-2378

journal_volume

29

pub_type

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