Dataset Information

Morphological Seed Characterization of Common (Phaseolus vulgaris L.) and Runner (Phaseolus coccineus L.) Bean Germplasm: A Slovenian Gene Bank Example.

ABSTRACT: Genetic resources comprised of 953 accessions of common (Phaseolus vulgaris L.) and 47 accessions of runner (Phaseolus coccineus L.) bean from the national Slovene gene bank were characterized using fourteen morphological seed descriptors. Seeds of each accession were evaluated for six quantitative characteristics: seed length, seed thickness, seed width, seed length/width ratio, seed width/thickness ratio, and 100 or 10 seed weight. Furthermore, seeds were evaluated using eight qualitative characteristics: seed colour; number of seed colours; primary/main seed colour; predominant secondary seed colour; distribution of secondary seed colour; seed veining; seed shape; and seed colour (primary and secondary) and coat pattern. For each, common, and runner bean collection, first four components within principal component analysis explained 75.03% and 80.16% of morphological variability, respectively. Regarding Ward's method and squared Euclidian distance, three clusters with the most distinct characteristics were established for each species. The results of morphological seed characterization indicate the origin (Andean, Mesoamerican, putative hybrids between gene pools) and domestication pathways of common and runner bean. This is the first study describing morphological seed characteristics of the entire common and runner bean germplasm conserved in one of the Central European bean collections. The results obtained in this study are serving as the useful information on genetic diversity of common and runner bean accessions at the Slovene gene bank, which could be used for development of new bean varieties for studied seed characteristics.

SUBMITTER: Sinkovic L

PROVIDER: S-EPMC6354170 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Morphological Seed Characterization of Common (Phaseolus vulgaris L.) and Runner (Phaseolus coccineus L.) Bean Germplasm: A Slovenian Gene Bank Example.

Sinkovič Lovro L Pipan Barbara B Sinkovič Eva E Meglič Vladimir V

BioMed research international 20190116

Genetic resources comprised of 953 accessions of common (Phaseolus vulgaris L.) and 47 accessions of runner (Phaseolus coccineus L.) bean from the national Slovene gene bank were characterized using fourteen morphological seed descriptors. Seeds of each accession were evaluated for six quantitative characteristics: seed length, seed thickness, seed width, seed length/width ratio, seed width/thickness ratio, and 100 or 10 seed weight. Furthermore, seeds were evaluated using eight qu ...[more]

PMID: 30792994

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Project description:The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.

Dataset Information

Morphological Seed Characterization of Common (Phaseolus vulgaris L.) and Runner (Phaseolus coccineus L.) Bean Germplasm: A Slovenian Gene Bank Example.

Publications

Morphological Seed Characterization of Common (<i>Phaseolus vulgaris</i> L.) and Runner (<i>Phaseolus coccineus</i> L.) Bean Germplasm: A Slovenian Gene Bank Example.

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