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Figures S1, S2, S3 and Table S1. Growth inhibition of 10 representative accessions in response to JA. Figure S1. for histogram of distribution of each trait. Figure S2. presents the variation of 5 traits between 10 representative’s accessions in non-treated and 5 μM JA treated condition. Figure S3. illustrated the percentage reduction of each trait after JA treatment compare to the non-treatment. Table S1. expressed the heritability coefficient of each traits. (DOCX 969 kb)

Figures S4, S5 and S6. GWAS for the effects of exogenous JA on RTL, SHW and TTW. Manhattan plot (A) and Quantile-quantile plot (B) for RTL (Figure S4), SHW (Figure S5) and TTW (Figure S6) in a whole (S.x.1) panel or Indica (S.x.2) or Japonica (S.x.3) subpanel. The blue line indicates the suggestive significance threshold, p = 3.0E-04. Black rectangle represent common significant SNPs within panels. (DOCX 1060 kb)

Figure S7. Haplotype analysis for qTTW5. (A) Linkage Disequilibrium heatmap in the peak region of association analysis GWAS for qRTW3. Significant SNP indicated as blue star in the photo and the pattern pairwise r2 of the associated SNPs in the QTL indicated with color code. Red color means SNPs are strongly associated to each other and yellow color means no association. The Linkage Disequilibrium heat map was created using the “LDheatmap” package in R (B) Population architecture of accessions based on the allelic combination significant SNPs in each QTL. Population architechture image is created by PopArt1.7 software . (C) Effect of allelic combination of 2 main haplotypes of each QTL on the value of interested traits. Number of accessions for each haplotype is indicated as (n). Welch Two Sample t-test was used to assess the differences between two haplotypes.*, **, *** indicated significant difference at p value

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.