1. Comparative analysis of five different methods to design a breed-specific SNP panel for cattle.
- Author
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Kumar H, Panigrahi M, Chhotaray S, Parida S, Chauhan A, Bhushan B, Gaur GK, Mishra BP, and Singh RK
- Subjects
- Animals, Breeding, Linkage Disequilibrium genetics, Cattle classification, Cattle genetics, Genotyping Techniques methods, Polymorphism, Single Nucleotide genetics
- Abstract
Single nucleotide polymorphisms (SNPs) have now replaced microsatellite markers in several species for various genetic investigations like parentage assignment, genetic breed composition, assessment for individuality and, most popularly, as a useful tool in genomic selection. However, such a resource, which can offer to assist breed identification in a cost-effective manner is still not explored in cattle breeding programs. In our study, we have tried to describe methods for reducing the number of SNPs to develop a breed-specific panel. We have used SNP data from Dryad open public access repository. Starting from a global dataset of 178 animals belonging to 10 different breeds, we selected five panels each comprising of similar number of SNPs using different methods i.e., Delta, Pairwise Wright's F
ST , informativeness for assignment, frequent item feature selection (FIFS) and minor allele frequency-linkage disequilibrium (MAF-LD) based method. MAF-LD based method has been recently developed by us for construction of breed-specific SNP panels. The STRUCTURE software analysis of MAF-LD based method showed appropriate clustering in comparison to other panels. Later, the panel of 591 breed-specific SNPs was called to their respective breeds using Venny 2.1.0 and UGent web tools software. Breed-specific SNPs were later annotated by using various Bioinformatics softwares.- Published
- 2021
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