Supplemental material for Ben Hassen et al., 2018

<p> Two Supplementary figures and seven Supplementary tables. Detailed description of each figure and table is presented in the first page of the file.<br></p

Unweighted neighbor-joining tree and the associated genetic structure estimated for <i>K</i> = 2 in the upper panel and <i>K</i> = 3 in the lower panel.

Temperate japonica is shown in red, tropical japonica in blue and admixed accessions are shown in purple. (PDF)</p

List of accessions in the two populations: The reference panel and the breeding population.

List of accessions in the two populations: The reference panel and the breeding population.</p

Comparison of the predictive ablities for eight morphological traits estimated by cross-validation on the reference panel and the 41 selected lines from the breeding population used as a validation set.

Control conditions are shown in black, and salt conditions in gray. Spearman’s rank correlation coefficients (ρ) are indicated.</p

Assessment of salinity tolerance under hydroponic conditions.

The image at the top represents half the 12 tanks for one replicate for the reference panel. The image at the bottom represents the three replicates for the selected genotypes of the breeding population. The control tanks are shown on the left and those for salt conditions are shown on the right. (PDF)</p

Fig 1 -

Unweighted neighbor-joining tree representing the dissimilarities between individuals composing the reference panel (black) and the breeding population (blue and green for the subset used for validation).</p

Fig 4 -

(A) Predictive abilities for stress response indices (iTrait) and ion mass fraction (Na and K) in the reference panel. Two different prediction methods are presented: GBLUP in orange and RKHS in gray. A Tukey boxplot is used to represent the data. (B) Scatterplot of estimates of predictive ability for indices and the level of genotype-by-environment interactions estimated by calculating the Spearman correlation coefficient for the same genotype in control and salt conditions.</p

S1 Fig -

Distribution in the rice genome of the informative markers for the complete set of 20,255 SNPs (upper panel) and the non-redundant set of 16,993 SNPs (lower panel). (PDF)</p

Distribution of minor allele frequency (MAF) for the 16,993 non-redundant SNPs in the two populations: The reference panel and the breeding population.

Distribution of minor allele frequency (MAF) for the 16,993 non-redundant SNPs in the two populations: The reference panel and the breeding population.</p

Summary of statistics for the 41 lines of the breeding population (BP41) for the various traits measured under control and salt conditions.

Summary of statistics for the 41 lines of the breeding population (BP41) for the various traits measured under control and salt conditions.</p