Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces
The common bean (<i>Phaseolus vulgaris</i> 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...
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MDPI AG
2019-09-01
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| author | Lucia Lioi Diana L. Zuluaga Stefano Pavan Gabriella Sonnante |
| author_facet | Lucia Lioi Diana L. Zuluaga Stefano Pavan Gabriella Sonnante |
| author_sort | Lucia Lioi |
| collection | DOAJ |
| description | The common bean (<i>Phaseolus vulgaris</i> 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 (F<sub>ST</sub>) 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. |
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| spelling | doaj.art-0ca421356b0b40959743ff62f275763f2022-12-22T04:09:50ZengMDPI AGDiversity1424-28182019-09-0111915410.3390/d11090154d11090154Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean LandracesLucia Lioi0Diana L. Zuluaga1Stefano Pavan2Gabriella Sonnante3Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, ItalyInstitute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, ItalyDepartment of Soil, Plant and Food Science, University of Bari ˝Aldo Moro˝, Via Amendola 165/A, 70126 Bari, ItalyInstitute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, ItalyThe common bean (<i>Phaseolus vulgaris</i> 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 (F<sub>ST</sub>) 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.https://www.mdpi.com/1424-2818/11/9/154<i>Phaseolus vulgaris</i>landracesgenotyping-by-sequencingSNPpopulation genetics |
| spellingShingle | Lucia Lioi Diana L. Zuluaga Stefano Pavan Gabriella Sonnante Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces Diversity <i>Phaseolus vulgaris</i> landraces genotyping-by-sequencing SNP population genetics |
| title | Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces |
| title_full | Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces |
| title_fullStr | Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces |
| title_full_unstemmed | Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces |
| title_short | Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces |
| title_sort | genotyping by sequencing reveals molecular genetic diversity in italian common bean landraces |
| topic | <i>Phaseolus vulgaris</i> landraces genotyping-by-sequencing SNP population genetics |
| url | https://www.mdpi.com/1424-2818/11/9/154 |
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