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 (r < 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.

Evaluation of single nucleotide polymorphisms identified through the use of SNP assay in Romanian and Chinese Holstein and Simmental cattle breeds

“…Thus, the highest number of polymorphic markers was observed on chromosome 1: 2252, 2237, 2256 and 2237 in HOL-CHN, HOL-RO, SIM-CHN and SIM-RO, respectively, and the smallest number on chromosome 25: 630, 627, 630 and 626, respectively, followed by chromosomes 27, 28, 29 and 26 (Table 2). Current results are in accordance with the previous studies, where the chromosome 1 had the highest and chromosomes 25-29 the lowest number of filtered SNPs (Zhu et al, 2013;Dash et al, 2017).…”

Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

“…The random blood samples were collected from different farms in the country in compliance with the guidelines and regulations of the Institutional Animal Ethics Committee (IAEC), National Bureau of Animal Genetics Resources (ICAR-NBAGR), Karnal (Supplementary Figure S1). After isolation of genomic DNA, estimation of quality and quantity was carried out as described earlier (Dash et al, 2018). DNA samples were genotyped at Sandor Lifesciences Pvt.…”

“…It has also been indicated that sample size as small as 4 -6 (Willing et al, 2012) and polymorphic SNP filtration (Colli et al, 2018;Utsunomiya et al, 2019) can mitigate ascertainment bias as long as the number of markers is sufficiently large as those under the current investigation. Earlier, in Indian dairy cattle breeds, we also tested bovine high-density genotyping array to assess its feasibility for Zebu cattle genomic studies (Dash et al, 2018). The genome proportion under autozygosity was almost equal in short and long ROH in all the breeds except Vechur.…”

Identification of breed-specific SNP panel in nine different cattle genomes.

“…To prepare the dataset we obtained the genotypic data from four high yielding indigenous milch cattle breeds, i.e., Tharparkar (12), Red Sindhi (10), Sahiwal (17) and Gir (24) with two dual-purpose breeds Hariana (10) and Kankrej (10) from Dryad repository (13) data for. ped/.map files accessed via WIDDE (Web-Interfaced next generation database for genetic diversity exploration).…”

“…Fifty percent of the SNPs of this assortment were found to be informative for genetic analysis of these cattle. The common SNPs with MAF ranging from 0.1 to 0.5 were approximately 50% and 34% for BovineHD and 54K Chips, respectively [10]. In another report, only SNPs in Hardy-Weinberg equilibrium, displaying the highest Minor Allele Frequency across all the thirty populations of French sheep breed (not associated with Mendelian errors in verified family trios) were selected.…”