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

Autor: Enciso-Rodríguez FE; Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia., Osorio-Guarín JA; Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia., Garzón-Martínez GA; Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia., Delgadillo-Duran P; Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia., Barrero LS; Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2020 Aug 26; Vol. 15 (8), pp. e0238383. Date of Electronic Publication: 2020 Aug 26 (Print Publication: 2020).
DOI: 10.1371/journal.pone.0238383
Abstrakt: 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 (HE: 0.35 to 0.36 and FIS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (FST: 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.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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