European <em>Phaseolus coccineus</em> L. landraces: Population Structure and Adaptation, as Revealed by cpSSRs and Phenotypic Analyses

<div><p>Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (<i>Phaseolus coccineus</i> L.), including the botanical varieties <i>albiflorus</i>, <i>bicolor</i> and <i>coccineus</i>, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties <i>albiflorus</i>, <i>bicolor</i> and <i>coccineus</i>, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.</p> </div

Cytoplasmic genetic structure.

<p>BAPS cluster assignments at K2 and K5 based on the cpSSR data of 331 European and 49 American accessions of <i>P. coccineus</i>. Beneath the K5 pattern, the three haplotypes shared between continents are indicated by black, grey and white bars. Abbreviations: <i>W</i> Wild; <i>DO</i> Domesticated; <i>GU</i> Guatemala; <i>MX</i> Mexico; <i>HO</i> Honduras; <i>CR</i> Costa Rica; <i>PT</i> Portugal; <i>ES</i> Spain; <i>IT</i> Italy; <i>NL</i> The Netherlands; <i>GM</i> Germany; <i>AT</i> Austria; <i>UR</i> Ukraine; <i>PL</i> Poland; <i>SK</i> Slovakia; <i>CR</i> Croatia; <i>HU</i> Hungary; <i>SL</i> Slovenia; <i>RO</i> Romania; <i>MD</i> Moldova; <i>GE</i> Georgia; <i>BG</i> Bulgaria; <i>AL</i> Albania; <i>No info</i> no information on country of origin.</p

Cytoplasmic and nuclear genetic structure.

<p>Comparison between the different clusterings of the accessions as inferred by BAPS at K2 (A) and at K5 and K6 (B) for cpSSR and nuSSR data. Only accessions shared between Spataro <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057337#pone.0057337-Spataro1" target="_blank">[20]</a> and the present study (158) are included; (C) TFPGA tree based on cpSSR and nuSSR Kullback–Leibler divergence matrices, as obtained with BAPS analysis.</p

Distribution and type of the American accessions of <i>P. coccineus</i> used in the present study.

<p>Distribution and type of the American accessions of <i>P. coccineus</i> used in the present study.</p

PCA analysis based on 260 accessions and 12 quantitative traits.

<p>The percentage of variation explained by each component is given next to the axis. Each accession is marked according to its membership to the different European regions. Varieties are also highlighted according to the colours given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057337#pone-0057337-g004" target="_blank">Figure 4</a>.</p

Varieties distribution across Europe.

<p>Geographic distribution of the 260 varieties identified as var. <i>albiflorus,</i> var. <i>coccineus</i> and var. <i>bicolor.</i></p

Varietal differences among the three varieties of <i>P. coccineus</i>.

<p>Different letters indicate means within columns that are significantly different (P <0.05; Student t test).</p

Correlation between latitude and flowering interval.

<p>Different colours indicate accessions from the two cpSSR groups A (orange) and E (blue) (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057337#pone-0057337-g001" target="_blank">Figure 1</a>), for which the regression lines (dashed) are illustrated. The trend line of the overall sample (grey continuous line) is also indicated. * P <0.0001</p

Phenotypic differences among the three varieties of <i>P. coccineus</i> used in the present study.

<p>Phenotypic differences among the three varieties of <i>P. coccineus</i> used in the present study.</p

CpSSR genetic diversity summary statistics for the American and European samples used in the present study.

<p>n_a =  number of alleles, total and rare (n_a <0.1); R_s  =  allelic richness; Hap/Ind  =  haplotype/accessions ratio; <i>H_E</i>  =  Nei’s (1978) gene diversity; <i>I_nor</i>  =  normalized Shannon-Weaver index of haplotype diversity.</p><p>Note: within the <i>R_s</i> columns, comparisons should be made between the values enclosed between the same bracket types.</p>*<p>when Δ is negative Europe > America.</p