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Comparative analysis of five different methods to design a breed-specific SNP panel for cattle.
- Source :
-
Animal biotechnology [Anim Biotechnol] 2021 Feb; Vol. 32 (1), pp. 130-136. Date of Electronic Publication: 2019 Jul 31. - Publication Year :
- 2021
-
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 <subscript>ST</subscript> , 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.
Details
- Language :
- English
- ISSN :
- 1532-2378
- Volume :
- 32
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Animal biotechnology
- Publication Type :
- Academic Journal
- Accession number :
- 31364913
- Full Text :
- https://doi.org/10.1080/10495398.2019.1646266