Scripts and reference tables of the ABC analysis

Contains the scripts needed to perform the simulations with ABCtoolbox and fastsimcoal for the ABC analysis, and the reference tables for each simulated model. ReadMe files are included in the directories

Polymorphism data

Microsatellite and nucleotide sequence data sets, used in the polymorphism study and the ABC analysis. ReadMe files describing the data are included in the directories

Intraspecific variability of carbon isotope discrimination and its correlation with grain yield in safflower: prospects for selection in a Mediterranean climate

<p>The goals of the present study were to obtain a first estimate of intraspecific variability of carbon isotope discrimination (Δ) in safflower, a thistle-like herbaceous plant, and to determine the statistical relationship between Δ and grain yield as well as its components in a collection of 45 accessions of different origins. Grain yield and aboveground biomass, harvest index, average grain weight, and Δ (measured on the bulk leaf organic matter) were investigated in experimental field conditions. A large variability was noted for all traits but a principal component analysis (PCA) allowed to identify several homogeneous groups of accessions. Average grain yield per plant varied between 1 and 39 g. Δ varied between 21.3 and 25.2 ‰, i.e. a large variation of 3.9 ‰. In our experiment, the variation of Δ was not significantly related to that of grain yield in the whole accession sample. However, we found contrasting trends for this relation within accession groups. These initial results motivate further experiments to assess more in depth correlation between Δ and yield in safflower and are encouraging regarding the possibility of using Δ as an effective selection index in safflower to obtain genotypes that efficiently consume water. This study also highlighted one accession that combines the two characters required in the Mediterranean regions, i.e. high yield performance and high water-use efficiency.</p

Acidic peatmoss substrate induces severe growth defect linked to the Shahdara allele.

<p>When grown on peatmoss at a pH close to 5, Shahdara is subject to severe growth and developmental arrest, necrosis and death, contrary to Bay-0 which develops normally. In the cross between these two strains, this phenotype is entirely controlled by a single locus (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002814#pgen.1002814.s001" target="_blank">Figure S1</a>), as confirmed by near-isogenic line ‘HIF084’ segregating solely for a region of chromosome 2.</p

Chemical complementation links growth defect with Mo shortage.

<p>Accessions with potentially functional (Bay-0, Col-0) and defective <i>MOT1</i> alleles (L<i>er</i>, Shahdara, <i>mot1.1</i>) were grown on peatmoss substrate watered with nutrient solution containing either traces of Mo (‘Control’) as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002814#pgen-1002814-g001" target="_blank">Figure 1</a>, or 1 mM Na₂MoO₄ (‘+Na₂MoO₄’). pH was checked to remain unchanged across treatments at ∼5.</p

Mutant analysis and allelic complementation confirms <i>MOT1</i> as the likely causative gene.

<p>Peatmoss phenotype of diverse genotypes is shown, including Bay-0 and Shahdara parental lines, <i>mot1.1</i> mutant and its wild-type genetic background (Col-0), and F1 plants from complementation crosses between these genotypes. Unlike other alleles, the Shahdara allele at <i>MOT1</i> is not able to rescue the mutant phenotype.</p

Microsatellite_data

microsatellite genotypes for the individuals of our stud

Posterior probability density distribution of the parameters of the demographic model inferred by ABC estimation.

<p>Data shown was obtained for the scenario “with migration”. The prior (black line) is used as a reference for the posterior distribution (blue lines) obtained from the rejection followed by the non linear regression. Parameters T, M and rho are scaled to the wild population effective size Ne_w.</p

Sorghum SSR

Dataset with the 321 sorghum samples and the 16 SSRs. The variety, site and farmer ID where the plant was collected are provided

Genetic diversity and selective neutrality tests for <i>PgHd3a</i>.

a<p>S: number of segregating sites. ^bSin: number of singletons. ^cθ: Watterson estimator of sequence diversity per site, π: average number of differences per site between two sequences, the diversity of the candidate genes was estimated for the non-coding (nc), synonymous (syn) and non-synonymous (nsyn) sites. ^dNumber of lineages with at least one singleton. ^eD and F* were calculated for the simulation using parameters randomly drawn from the posterior distribution.^f<i>P-</i>values were computed for unilateral tests as <i>P</i>< or > than the observed value according to the sign of the statistics without correction for multiple tests.</p