Diversification and population structure in common beans (Phaseolus vulgaris L.)

Abstract

Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.

Figure 1. Population structure analysis for 104 wild accessions of common bean and 4 control genotypes based on microsatellite marker analysis.

K-values of 2 to 5 sub-populations are shown to right and naming of wild common bean genepools given below and assignment to Andean or Mesoamerican groups shown above.

Figure 2. Neighbor-joining dendogram of wild accessions of common beans with sub-populations based on population structure analysis shown in previous figure.

Figure 3. Geographical distribution of the collections sites for wild bean accessions genotyped in this study (A) and their assignment by principal component analysis to five genepools based on population structure analysis with microsatellite markers (B).

Each genepool is shown with a different symbol/color.

Figure 4. PCoA analysis of the associations between wild (W) common beans and races of cultivated (C) common beans with panel A showing only genepool and wild versus cultivated bean differences and panel B showing the same analysis but with aggregates of cultivated races and wild sub-populations as defined by the legend.

A three letter code is used to name the wild populations, while the conventions of Blair et al. were used for races: DJ: Durango-Jalisco, M: Mesoamerica, NG: Nueva-Granada, P: Peru, and G: Guatemala.

Figure 5. Population structure analysis with the combined dataset of wild and cultivated accessions in A) the Andean genepool and B) the Mesoamerican genepool, with race and sub-population abbreviations as in previous figure.