Table 1.
Taxonomic classification of accessions.
Table 2.
Distribution of SNPs per chromosome, before and after editing for call-rate and MAF.
Table 3.
Recorded traits.
Fig 1.
Stacked barplot for the ancestry of the available 391 rice accessions with K = 5.
Fig 2.
Neighbour-joining trees of the 391 accessions (left) and of the 153 (centre) and 93 (right) subsets used for plant & grain and root phenotyping respectively.
Temperate japonica accessions in blue, tropical japonica in red, indica in green, aus in violet, and aromatic in black.
Fig 3.
Phenotypic correlations among plant morphology, grain quality and root traits.
Table 4.
Descriptive statistics of collected phenotypes.
Fig 4.
Average LD as a function of inter-marker distance estimated in the panel of 391 accessions.
Table 5.
Most significant associations between SNP genotypes and shoot, grain and root phenotypes in the analysed rice accessions.
Fig 5.
Manhattan and Q-Q plots of GWAS results for plant morphology traits.
Fig 6.
Manhattan and Q-Q plots of GWAS results for grain quality traits.
Fig 7.
Manhattan and Q-Q plots of GWAS results for root traits.
Fig 8.
Manhattan and Q-Q plots of GWAS results for thick root traits.
Fig 9.
Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.
Fig 10.
Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.