Additional file 1: Figure S1. of Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Mean minimum–maximum normalized values for all analyzed traits in parental lines and RILs. Fig. S2 Some examples of RILs and the parental lines at seedling stage, 27 days after sowing. Fig. S3 Coefficient of variation for the different traits measured. Fig. S4 PCA analysis of the phenotype data of the population. Fig. S5 Expression patterns of the top 1 % of genes (anti-)correlated with the different traits. Fig. S6 Overrepresented MapMan categories of top 1 % of genes (anti-)correlated with phenotypic traits. Fig. S7 Overrepresented MapMan categories of top 1 % of genes (anti-)correlated with final leaf size traits. (PDF 1976 kb

A Late Bronze to Early Iron Age Tomb at Sahem, Jordan

Quantitative data for MM founders’ sequencing and expression. For sequencing, raw reads count and mean and modal coverage (in folds) are given. For expression data, raw reads numbers are given for each biological replica (B1, B2, B3). (XLSX 9 kb

Additional file 23: Figure S13. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Linkage disequilibrium within the flowering time QTL confidence interval. Panel a shows the heat map considering all imputed SNPs in the region. From white to red, increasing LD. Along the diagonal, SNP marker index, not proportional to physical position (noted on edges). ZCN8 position is marked with an asterisk. The haplotype of highest significance is framed in blue. Panel b shows mean LD in a sliding window. On the x axis, physical position on the genome. The red box marks the haplotype of highest significance according to the association approach. LD is generally low in the QTL region, but a few distinctive peaks are visible: the most central to the QTL interval is short upstream ZCN8 (position marked with *), which lacks imputed SNPs. (PDF 2509 kb

Additional file 5: Figure S3. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Unrooted phylogeny of the MM population, magnified from Fig. 3a. Founders’ placement is highlighted with the corresponding colors. Note that genetic distances between MM lines are evenly distributed throughout. (PDF 20148 kb

Additional file 11: Table S5. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Summary of power simulation results with varying sample sizes (100, 200, 300, 400, 500). For each simulated QTL, the effect and the variance explained are given. The power to detect each QTL is averaged on 400 independent runs (100 for each of MAF 0.125, 0.25, 0.375, and 0.5). Results are given for h 2 = 0.4 and 0.7. (XLSX 17 kb

Additional file 6: Figure S4. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Structure in the MM population. A principal components (PC) analysis on MM founders genotypes is shown in panel a. PC one to five are shown, each square representing one founder with colors according to those given in Fig. 1. Two replicas for each founder are shown. As expected, PC loadings (and structure) for founders are higher than those of RIL. Panel b shows PC one to five for the MM lines. Breeding subfamilies are depicted in different colors. PC 1 provides a slight separation in two clusters, but the highest PC loading is of only 1.7%. The distribution of the PC loadings for PC 1–100 in the MM lines shows a smooth decrease throughout in panel c. Panel d reports the outcome of a discriminant analysis of principal components (DAPC) over the MM lines. The lowest BIC values are assigned to one-two clusters, confirming the absence of structuration in the MM population. (TIFF 3269 kb

Additional file 19: Figure S12. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

QTL scan for days to pollen shed. In panel a, the full model scan. On the x axis, the physical position from Chr 1 to 10. On the y axis, the LOD score. Red and green thresholds represent strong (P <0.01) and suggestive (P <0.63) thresholds by 1,000 permutations, respectively. In panel b, the scan for the same trait including the highest QTL in panel a as a covariate. (PDF 1618 kb

Additional file 14: Figure S8. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Distribution of phenotypic estimated values across the MM lines. Frequency classes of MM lines are chosen on the basis of the standard error of the mean for each traits. Grain yield is ytr = y0.5 transformed to obtain homoscedasticity of the residuals. Plant height and ear height are in the range of 76.8–252.1 cm and 32.3–164.91 cm, respectively. Days to pollen shed variation spans 16 days. (TIFF 578 kb

Additional file 13: Table S6. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Phenotypic estimated values of the eight founders and 529 MM lines analyzed for days to pollen shed (PS), plant height (PH), ear height (EH), and transformed grain yield (GYrad). (XLSX 36 kb