Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs.

Sofía I Deperi,Norma C Manrique-Carpintero,M Cecilia Bedogni,Ruofang Zhang,Martín E Tagliotti,Marcelo A Huarte,Joseph Coombs,David Douches,Xiu-Qing Li

doi:10.1371/journal.pone.0194398

Abstract

The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.

Highlights

Modern potato cultivars were developed from a few clones brought from the American continent to Europe in the XVI century
Allelic frequencies of subpopulations detected by discriminant analysis of principal components (DAPC) were well differentiated (Fst = 0.118), and homozygotes and heterozygotes were balanced, (Fis = -0.022)
Genetic variability is essential to breeders for the generation of improved varieties resistant to diseases and adapted to adverse environmental conditions, without neglecting yield and industrial quality

Summary

Introduction

Modern potato cultivars were developed from a few clones brought from the American continent to Europe in the XVI century. Cross-breeding of potato and systematic utilization of related wild species has been made after the late blight epidemics [2] These species have great variability for many desirable agronomic characters [1, 3,4,5,6,7]. The genetic characterization of available potato populations allows us to assess their diversity and structure and to identify the genotypes that could work as a source of new alleles in potato breeding programs The aim of these programs has been to incorporate resistance to biotic and abiotic stresses, as well as to develop better processing qualities and combine these characters with high yield and commercial quality [10], using conventional or molecular

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Conclusion