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Additional file 2. Fig. S1: Genome-wide association (GWA) mapping results for rice sheath blight disease ratings based on an imputed 3,463,224 SNP dataset. Field and greenhouse studies were conducted in both Stuttgart, Arkansas (AR) USA and Nanning, China (NC) with Arkansas field studies being conducted in 2016 and 2017, and Nanning field studies in 2018. Manhattan (left) and Q-Q (right) plots are grouped by study environment a) Arkansas field 2016, b) Arkansas field 2017, c) Arkansas field both years combined, d) Nanning field 2018, e) Arkansas greenhouse, and f) Nanning greenhouse. Within each environment the plots are arranged in the following order by panel Indica subspecies (INDAUS), aus (AUS), Indica (IND), Japonica subspecies (JAP), temperate japonica (TEJ), tropical japonica (TRJ) and all RDP1 accessions (395). In the Manhattan plots the X axis shows the SNP positions across the 12 rice chromosomes and the Y axis is the –log10 (p) value for each SNP. The black horizontal line represents the –log10(p) significance threshold at 5. Black arrows identify the significant peak SNPs with regions >100 Kb comprising the 18 GWA ShB-QTL. The 21 target SNPs listed in Table 3 are identified by red arrows. (If two or more peak SNPs were in close proximity in a given QTL region, the peaks were denoted by a single arrow.) Fig. S2: Genome-wide association (GWA) mapping results for days to 50% heading, plant height and culm habit based on an imputed 3,463,224 SNP dataset. The data was collected from field studies conducted at Stuttgart, Arkansas (AR) in 2016 and 2017, and Nanning, China (NC) in 2018. Manhattan (left) and Q-Q (right) plots are grouped by the trait evaluated in the field study as follows: a) days to heading, b) plant height and c) culm habit. Within each trait the plots are arranged by field study environment Arkansas field 2016 (AR16), Arkansas field 2017 (AR17), Arkansas field both years (ARall) and Nanning field 2018 (NC18), Culm habit was only recorded from the Arkansas field study in 2017. In the Manhattan plots the X axis shows the SNP positions across the 12 rice chromosomes and the Y axis is the –log10 (p) value for each SNP. The black horizontal line represents the –log10(p) significance threshold at 5. Black arrows indicate the significant peak SNPs identified by the GWA mapping of the RDP1 accessions (395) with a region >100 Kb. Details are in Table S3. (If two or more peak SNPs were in close proximity, they were denoted by a single arrow.) Fig. S3: Manhattan (left) and Q-Q (right) plots identifying the 15 TN and 14 PN QTL regions identified by GWA analyses using an imputed 3,463,244 SNP dataset (Table 4). In the Manhattan plots the X axis shows the SNP positions across the 12 rice chromosomes and the Y axis is the –log10 (p) value for each SNP. The black horizontal line represents the –log10(p) significance threshold at 5. Black arrows indicate peak SNPs within the indicated QTL regions. The plots are organized by trait with the TN results in plots A through F and PN results in plots in G through L. Subpopulation abbreviations are INDAUS (Indica subspecies), JAP (Japonica subspecies), AUS (aus), IND (Indica), TEJ (temperate japonica), and TRJ (tropical japonica)

Additional file 1: Supplementary Figure 1. Pearson correlation among ionomics and agronomic traits. (a) Ionomics in flooded environment and agronomic traits. (b) Ionomics in unflooded environment and agronomic traits. (c) Ionomics in flooded environment (with 1 as suffix) and unflooded environment (with 2 as suffix).

Additional file 2: Supplementary Figure 2. (a). Genome-wide association analysis for As with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). Red arrow indicates published gene, black arrow indicates candidate gene. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (b) Genome-wide association analysis for Cd with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). Black arrows indicate candidate genes. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (c) Genome-wide association analysis for Cd with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). Black arrows indicate candidate genes. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (d) Genome-wide association analysis for Cu with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (e) Genome-wide association analysis for Co with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (f) Genome-wide association analysis for Fe with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni -corrected significance thresholds and SNPs at −log10(P) = 8.51. (g) Genome-wide association analysis for K with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (h) Genome-wide association analysis for Mo with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (i) Genome-wide association analysis for Mo with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (j) Genome-wide association analysis for Ni with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (k) Genome-wide association analysis for Ni with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni -corrected significance thresholds and SNPs at −log10(P) = 8.51. (l) Genome-wide association analysis for Rb with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (m) Genome-wide association analysis for Sr with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (n) Genome-wide association analysis for Zn with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (o) Genome-wide association analysis for Zn with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51.