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

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

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

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

Estimates of predictive ability for performances in the two sets of conditions (CTRL and SALT) for the reference panel.

Performances were predicted with multi-environment (black) or single-environment (gray) models. Two different prediction methods were used: GBLUP and RKHS. The traits considered were: Number of tillers (TIL), leaf length (LL), leaf area (LA), specific leaf area (SLA), root length (RL), root dry weight (ROOT), shoot dry weight (SHOOT) and the ratio of root-to-shoot dry weights (R_S). The bars represent the average predictive ability over 100 replicates, and the error bars represent the standard error of the mean.</p

Boxplot of genomic estimated breeding value (GEBV) for the eight morphological traits in the breeding population of 393 lines.

The 41 lines selected for the validation experiment are represented in black and the rest of the population is shown in gray. Two prediction methods (GBLUP and RKHS) and two models (single- and multi-environment) were compared. (PDF)</p

Relationship between predictive abilities estimated by cross-validation on the reference panel and those estimated with the subset (41 lines) of the breeding population.

Two models (single- and multi-environment) and two methods (GBLUP and RKHS) were evaluated. (PDF)</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