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

ABSTRACT: 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.

SUBMITTER: Enciso-Rodriguez FE 

PROVIDER: S-EPMC7449456 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature