Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm.

Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from "pure" accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with "pure" accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.

Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes.

We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.

Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean.

Reduction in pod shattering represents a key component of the domestication syndrome in common bean (Phaseolus vulgaris) and makes this domesticate dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene (St) linked to the presence/absence of pod suture fibers affecting pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of this study was to identify a candidate gene for St. In Arabidopsis thaliana, INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in P. vulgaris and placed on the common bean map using two recombinant inbred populations (BAT93 × Jalo EEP558; Midas × G12873). Although PvIND maps near the St locus, the lack of complete cosegregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlated with the dehiscent/indehiscent phenotype suggests that PvIND may not be directly involved in pod shattering and may not be the gene underlying the St locus. However, PvIND may be closely linked to an as yet unidentified regulatory element at the St locus. Alternatively, a more precise phenotyping method taking into account quantitative trait variation needs to be developed to more accurately map the St locus.