Table 1.
Descriptive statistics for the genetic linkage map of the parental genotype (H12 hybrid) of the F2 mapping population.
Fig 1.
Results from QTL analysis of the F2 mapping population.
The LOD score patterns for total height (blue) and stem straightness (orange) over the 12 linkage groups of maritime pine are represented. The location of the QTLs (p < 0.05 at the genome wide level) is indicated by vertical dotted lines.
Table 2.
QTL results from the analysis of the F2 mapping population for stem straightness (STR).
Location (cM) of QTLs on linkage groups with 95% Bayesian credible intervals, % variance explained by the QTL (PEV), log10 likelihood ratio scores (LOD) and grandparental origin of the favorable effect (Landes (L) or Corsican (C)) are presented. For the additive and dominance effects, the proportions in standard deviation is indicated in parenthesis.
Table 3.
QTL results for the analysis of the G2 mapping population for height increment.
Location (cM) of QTLs on linkage groups with 95% Bayesian credible intervals, % variance explained by the QTL (PEV) and log10 likelihood ratio scores (LOD) are presented. For the allelic substitution effect, the proportion of standard deviation is indicated in parenthesis.
Fig 2.
Q-Q plots for the three different association models.
Simple model (red dots), FASTA model (closed triangles) and Grammar-GAMMA model (open triangles). For both the FASTA and Grammar-GAMMA models, we used matrix A (in blue) or matrix G (in green) to take relatedness between individuals into account.
Fig 3.
Distribution of p-values (on a negative log10 scale) over the 12 linkage groups from the genome-wide association analysis (panel A) and the absolute effect of markers in the Bayesian LASSO model (panel B) for height and stem straightness. In panel A, the horizontal dashed line represents the threshold at p = 0.001 and the horizontal dotted line represents the threshold at q = 0.10. In panel B, the associations for which p <0.001 are indicated by vertical dotted lines. Only mapped markers are displayed.
Fig 4.
Position of the QTLs detected by LA and LD mapping on the Pinus pinaster composite genetic map.
For LA mapping, QTLs for stem straightness (STR) are shown in orange and QTLs for height increment (HI) are shown in blue. The whiskers indicate the 95% credible interval around QTL peaks. The locations of markers significantly associated with height (HT, purple) and stem straightness (STR, red) are also indicated. On linkage group 2, the two significant associations for HT are co-located (158 cM and 158.1 cM).
Table 4.
Significant (p<0.001) marker-trait pairs and their location on the genetic map, for height (HT) and stem straightness (STR).