A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding.

ABSTRACT: Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by

SUBMITTER: Selga C 

PROVIDER: S-EPMC7824009 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature