Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

Gina A Garzón-Martínez,Jaime A Osorio-Guarín,Paola Delgadillo-Durán,Franklin Mayorga,Felix E Enciso-Rodríguez,David Landsman,Leonardo Mariño-Ramírez,Luz Stella Barrero

doi:10.1016/j.plgene.2015.09.003

Abstract

The genus Physalis is common in the Americas and includes several economically important species, among them is Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNP) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

Highlights

The genus Physalis consists in more than 90 species, native of the Americas, being Mexico the center of diversity of the husk tomato (Vargas-Ponce et al, 2010)
Young leaves of 222 plants belonging to 47 Physalis peruviana accessions and 13 related taxa were collected from an in vitro germplasm collection maintained at the Colombian Corporation for Agricultural Research (CORPOICA) (Table 1, Supplementary Table 1)
Monomorphic markers on agarose gels (15 COSII and 18 Immunity Related Genes (IRGs)) based on their size and random distribution across the tomato chromosomes were selected for sequencing in order to uncover Single Nucleotide Polymorphism (SNPs) on a 64-plant panel (Table 2, 3)

Summary

Introduction

The genus Physalis consists in more than 90 species, native of the Americas, being Mexico the center of diversity of the husk tomato (Vargas-Ponce et al, 2010). The genus includes different species with nutritional, nutraceutical and commercial interests. Some Physalis species have been widely recognized by their nutraceutic and economic importance, little is known about their genetic diversity at the molecular level, mainly because of the lack of available markers in accordance with their current status as orphan species. Berdugo et al (2015), used 328 COSII and 154 Immunity Related Genes (IRGs) to evaluate an F1 population generated between contrasting pathogen response parents. This population showed a total of 127 alleles with an average of 3.18 per locus, a PIC of 0.358 and high values of heterozygosity (Ho: 0.737 and He: 0.449)

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