An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

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.

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Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites

Plant Genetic Resources ◽

10.1017/s1479262110000420 ◽

2011 ◽

Vol 9 (01) ◽

pp. 86-96 ◽

Cited By ~ 17

Author(s):

Lucy M. Díaz ◽

Héctor F. Buendía ◽

Myriam C. Duque ◽

Matthew W. Blair

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Common Bean ◽

Gene Pool ◽

Major Gene ◽

Gene Pools ◽

Silver Stain ◽

Fluorescent Marker ◽

Fluorescent Markers

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgarisL.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescentversusnon-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

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Genetic diversity, population structure, and differentiation of Siberian larch, Gmelin larch, and Cajander larch on SSR-marker data

Russian Journal of Genetics ◽

10.1134/s1022795412120095 ◽

2013 ◽

Vol 49 (2) ◽

pp. 178-186 ◽

Cited By ~ 15

Author(s):

N. V. Oreshkova ◽

M. M. Belokon ◽

S. Jamiyansuren

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Marker ◽

Siberian Larch ◽

Marker Data

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SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis

Molecular Genetics and Genomics ◽

10.1007/s00438-016-1182-3 ◽

2016 ◽

Vol 291 (3) ◽

pp. 1277-1291 ◽

Cited By ~ 11

Author(s):

Paula Arielle M. R. Valdisser ◽

Georgios J. Pappas ◽

Ivandilson P. P. de Menezes ◽

Bárbara S. F. Müller ◽

Wendell J. Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Common Bean ◽

Structure Analysis ◽

Rad Sequencing ◽

Snp Discovery ◽

Population Structure Analysis

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Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽

10.1371/journal.pone.0243238 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243238

Author(s):

Wilson Nkhata ◽

Hussein Shimelis ◽

Rob Melis ◽

Rowland Chirwa ◽

Tenyson Mzengeza ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Bean ◽

Southern Africa ◽

Crop Improvement ◽

Phenotypic Expression ◽

Snp Markers ◽

High Yield ◽

Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

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Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽

10.3390/genes11111298 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1298

Author(s):

Caléo Panhoca de Almeida ◽

Jean Fausto de Carvalho Paulino ◽

Sérgio Augusto Morais Carbonell ◽

Alisson Fernando Chiorato ◽

Qijian Song ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Common Bean ◽

Gene Diversity ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

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