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

Abstract

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.

Fig 1. Two-dimensional principal coordinate analysis (PCoA) of SSR diversity in 192 U.S. commercial lines of common bean.

A. PCoA1 vs. PCoA2. B. PCoA1 vs. PCoA3. The position of control genotypes for each gene pool is shown. The distribution of major market classes (LRK light red kidney, DRK dark red kidney, WK white kidney, GB green bean, Black, SW small white, Navy, GN great northern, and Pinto) based on pedigree data is also shown.

Fig 2. Population structure analysis for 192 advanced cultivars of Andean and Mesoamerican common bean races based on SSRs analysis.

K-values of subpopulations are shown to right and naming of common bean commercial market class given below. Each individual is represented by a vertical line, and cluster assignments are indicated by color. Bar graphs were developed with the program DISTRUCT.

Fig 3. Neighbor-joining tree of SSRs diversity for the 192 advanced cultivars based on the C. S. Chord distance.

Each branch is color-coded according to membership into the K = 5 groups identified by STRUCTURE (same colors as in Fig 2). K1 (Blue): Kidney market class; K2 (Green): Green bean market class; K3 (Orange): Small-seeded (white, black) market class; K4 (Pink): Pinto and great northern market classes; K5 (Yellow): Pinto and great northern market classes.

Fig 4. Results of DAPC applied to the 192 commercial advanced cultivars of common bean.

A. Bayesian Information Criteria (BIC) for increasing values of the number of clusters. The chosen number of clusters was K = 7. B. Scatterplot of the first two principal components of the DAPC on the common bean collection. Individuals are represented by symbols according to their market class. Colours and inertia ellipses identify the clusters. C. Loading plot generated from using all 58 SSR, with the horizontal line representing an arbitrary threshold value of .002. Illustrates which SSR contributed most to the individual principle component analysis.

Fig 5

A. Results of DAPC applied to a worldwide germplasm collection of 349 wild and domesticated landraces of common beans [7]. B. Scatterplot of the projection of the 192 common bean advanced cultivars on the genetic clusters identified by DAPC on the worldwide germplasm collection. The clusters are represented by their inertia ellipses.