Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial culti...

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Bibliographic Details
Published in:PloS one 2020-08, Vol.15 (8), p.e0238383-e0238383
Main Authors: Enciso-Rodriguez, Felix E, Osorio-Guarin, Jaime A, Garzon-Martínez, Gina A, Delgadillo-Duran, Paola, Barrero, Luz Stella
Format: Article
Language:English
Subjects:
Biology and Life Sciences
Breeding
Conservation
Cultivars
Deoxyribonucleic acid
DNA
DNA methylation
DNA sequencing
Ecology and Environmental Sciences
Gene expression
Gene flow
Genetic aspects
Genetic diversity
Genomes
Genotypes
Genotyping
Germplasm
Identification and classification
Methods
Nucleotides
Optimization
Pathogens
Physalis peruviana
Physical Sciences
Plant breeding
Population
Population structure
Potatoes
Principal components analysis
Research and Analysis Methods
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Subpopulations
Taxa
Tomatoes
Winter cherry
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Summary:A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (H.sub.E : 0.35 to 0.36 and F.sub.IS : -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (F.sub.ST : 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0238383