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Research article - Peer-reviewed, 2021

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

Selga, Catja; Koc, Alexander; Chawade, Aakash; Ortiz, Rodomiro

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 two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.

Keywords

linkage disequilibrium pruning; genomic selection; genotyping; GWAS; potato breeding

Published in

Plants
2021, volume: 10, number: 1, article number: 30

Authors' information

Swedish University of Agricultural Sciences, Department of Plant Breeding
Swedish University of Agricultural Sciences, Department of Plant Breeding
Swedish University of Agricultural Sciences, Department of Plant Breeding
Ortiz, Rodomiro (Ortiz Rios, Rodomiro Octavio)
Swedish University of Agricultural Sciences, Department of Plant Breeding

UKÄ Subject classification

Genetics and Breeding
Plant Biotechnology

Publication Identifiers

DOI: https://doi.org/10.3390/plants10010030

URI (permanent link to this page)

https://res.slu.se/id/publ/109402