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, 13 (3), e0194398
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Discriminant Analysis of Principal Components and Pedigree Assessment of Genetic Diversity and Population Structure in a Tetraploid Potato Panel Using SNPs

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Discriminant Analysis of Principal Components and Pedigree Assessment of Genetic Diversity and Population Structure in a Tetraploid Potato Panel Using SNPs

Sofía I Deperi et al. PLoS One.

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Discriminant analysis of principal components (DAPC) for 231 genotypes of the germplasm collection of INTA Balcarce potato breeding program.
The axes represent the first two Linear Discriminants (LD). Each circle represents a cluster and each dot represents an individual. Numbers represent the different subpopulations identified by DAPC analysis.
Fig 2
Fig 2. Discriminant analysis of principal components (DAPC) for 231 genotypes of the germplasm collection of INTA Balcarce potato breeding program.
(a) subpopulation 1 (b) subpopulation 2. The axes represent the first two linear discriminants (LD). Circles represent groups and dots represent individuals. Numbers represent the different subpopulations identified by DAPC analysis.
Fig 3
Fig 3. Dendrogram from Nei genetic distance matrix for 231 genotypes of the germplasm collection of INTA Balcarce potato breeding program.
Dendrogram of the whole population divided in clusters. In the X axe are represented the genetic distances between groups and individuals. In the Y axe are represented the subpopulations in which the population was divided.

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References

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Publication types

Grant support

This study was supported by Fund for Scientific and Technological Research (FONCyT - AGENCIA) PICT 2610/2010, www.agencia.mincyt.gob.ar/frontend/agencia/fondo/foncyt, to MAH; and National Institute for Agricultural Technology, Argentina (INTA) PNHFA 1106074, www.inta.gob.ar, to MAH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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