Table 1.
Diversity statistics computed using 29911 Panzea SNP markers over the whole panel and five main genetic groups.
Figure 1.
Genome-wide linkage disequilibrium between all loci within and between chromosomes.
The upper triangle corresponds to the LD r2 measure calculated with Plink [50], the lower triangle to the LD r2s measure [34] corresponding to r2 corrected for structure, using the Q matrix obtained with STRUCTURE software [40], [41] and 55 SSRs. Values above 0.2 are highlighted by colored dots.
Table 2.
Extent of linkage disequilibrium and number of markers needed to reach average r2 = 0.1 for individual chromosomes and the whole genome.
Figure 2.
Manhattan plot for female flowering (FFLW8) associations across the whole genome.
P-values were obtained with the mixed model including the structure matrix obtained using STRUCTURE software and 55 SSRs and the kinship matrix obtained with 94 SSRs and IBS measure. Horizontal dashed line indicates Bonferroni-corrected 5% significance threshold.
Figure 3.
Distribution of SNP effects (GDD) according to the early allele frequency.
In this figure, 673 markers with P-value<10−3 are represented. (A) For all inbred lines (rows) and SNPs (columns), red and blue colors correspond to the presence of late and early alleles, respectively. (B) The absolute SNP effect versus the frequency of the early allele for significant associations. Different colors correspond to different P-value thresholds.
Table 3.
Regions associated with FFLW8 (P-value below 10−5)) and/or under selection (log10(PO) above 0.5).