title: Genetic diversity and population structure inPhysalis peruvianaand related taxa based on InDels and SNPs derived from COSII and IRG markers.
abstract: The genusPhysalisis common in the Americas and includes several economically important species, among themPhysalis peruvianathat produces appetizing edible fruits. We studied the genetic diversity and population structure ofP. peruvianaand 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 (SNPs) 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 forP. peruvianawith 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 FSTwas 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation amongP. peruvianaand 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 theP. peruvianaaccessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation inPhysalisgermplasm for assisting conservation and crossbreeding strategies.
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Gina A
authors.initials: GA
authors.lastname: Garzón-Martínez
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Osorio-Guarín
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Paola
authors.initials: P
authors.lastname: Delgadillo-Durán
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Franklin
authors.initials: F
authors.lastname: Mayorga
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Felix E
authors.initials: FE
authors.lastname: Enciso-Rodríguez
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, United States of America, Bethesda, MD, USA.
authors.forename: David
authors.initials: D
authors.lastname: Landsman
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, United States of America, Bethesda, MD, USA.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mariño-Ramírez
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia ; Agrobiodiversity Department, National Direction of Research and Development, CORPOICA.
authors.forename: Luz Stella
authors.initials: LS
authors.lastname: Barrero
keywords: COSII; Cape gooseberry; Genetic variation; IRGs; SNPs; germplasm