Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought b...

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Bibliographic Details
Published in:Diversity (Basel) 2019-09, Vol.11 (9), p.154
Main Authors: Lioi, Lucia, Zuluaga, Diana L., Pavan, Stefano, Sonnante, Gabriella
Format: Article
Language:English
Subjects:
Adaptation
Beans
Divergence
Domestication
Enzymes
Gene polymorphism
Gene sequencing
Genetic distance
Genetic diversity
Genomes
Genotyping
genotyping-by-sequencing
Germplasm
Hybridization
landraces
Legumes
Linkage disequilibrium
Markers
Most probable number
Nucleotides
Nutrients
Phaseolin
Phaseolus vulgaris
Polymorphism
population genetics
Proteins
Seeds
Single-nucleotide polymorphism
SNP
Software
Structural analysis
Subgroups
Subpopulations
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Summary:The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.
ISSN:1424-2818
1424-2818
DOI:10.3390/d11090154