Co-localization of significant SNPs and haplotypes detected by the three GWAS methods with QTL for heat tolerance during the reproductive phase detected in biparental crosses.

<p>Blue: Sm-GWAS, Green: Hap-GWAS, Black: BL-GWAS and Red: QTL.</p

Projection of the contribution of the 20 phenotypic traits on the plan of the first two axes of a Principal Component Analysis.

<p>Traits subjected to three methods of GWAS are indicated in blue.</p

Results of the survey of genome annotation within an interval of 100 kb (50 kb downstream and 50 kb upstream) around each locus associated with SPKST under 2 or 3 GWAS methods.

<p>Results of the survey of genome annotation within an interval of 100 kb (50 kb downstream and 50 kb upstream) around each locus associated with SPKST under 2 or 3 GWAS methods.</p

Co-localization of the loci significantly associated with one of the eight phenotypic traits as detected by three GWAS methods.

<p>Co-localization of the loci significantly associated with one of the eight phenotypic traits as detected by three GWAS methods.</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

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

Distribution of genomic estimated breeding value (GEBV) for Na and K mass fraction and their ratio (Na/K) in the breeding population of 393 lines.

The 41 breeding lines selected for the validation experiment are represented in green and the rest of the population is shown in gray. Two different prediction methods were used: GBLUP and RKHS. (PDF)</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

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

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