For each trait, the phenotypic values in homozygotes (in grey; n=72) were normalised relative to the mean phenotypic values in heterozygotes (in black; n=86). The point represent the mean and the …
(A) We randomly crossed A. lyrata individuals from the PIN, TSS, and IND populations in North America (left) and A. halleri from the Nivelle (middle) and Mortagne (right) populations. Individuals …
(A) The two topologies of interest cluster haplotypes either by the S-allele to which they are linked (top) or by the populations where they came (bottom). Different S-alleles are represented by …
The S-allele to which the SNPs are linked are represented by different symbols. The right panels show the analysis on control regions, each time matching the number of SNPs with that of the …
The S-allele to which the SNPs are linked are represented by different symbols. The right panels show the analysis on control regions, each time matching the number of SNPs with that of the …
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths …
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths …
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths …
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths …
Left: mean FST (lines) and FST by pair (point) analysed among S-alleles (grey) or among populations (black) in 5 kb windows in the S-locus flanking regions. Right: distribution (count) of FST in the …
Each dot corresponds to an SNP showing statistically significant association (top 0.1%) with a given S-allele. The left panel confirms that SNPs physically linked to the S-locus (in red) are …
Each dot represents the mean number of mutations observed among haplotypes linked to one S-allele in one population. The correlations evaluated by a generalised linear model (GLM) are represented by …
Each dot represents the value obtained for haplotypes linked to one S-allele in one population. The correlations evaluated by a generalised linear model (GLM) are represented by lines, with …
Number of fixed (A), segregating (B), and total (C) deleterious mutations linked to S-alleles at four different levels of dominance (I<II < III<IV). The means (bold lines) were estimated per S-allele…
The test is performed relative to the expected proportion of homozygous genotypes in the offspring (25% when both parents are heterozygous; 50% when one of the parents is homozygous and the other …
S-allele | Level of dominance | Number of seedlings having reached the reproductive stage | Observed proportion of homozygotes | Ratio of the observed to expected proportion of homozygous genotypes (p-value*) | Number of heterozygotes with the S-allele (p-values*) |
---|---|---|---|---|---|
Ah01 | I | 35 | 0.29 | 1.14 (0.76) | 19 (0.40; 0.90) |
Ah03 | II | 27 | 0.074 | 0.3 (0.02) | 17 (1; 0.69) |
Ah04 | III | 96 | 0.479 | 0.96 (0.39) | 50 |
Values departing from Mendelian expectations are figured in bold. For Ah04, the maternal parent was Ah04/Ah04, so all heterozygous offspring carried the S-allele.
p-Values were obtained after 10,000 random permutations, respectively.
Protocol used.
(a) Crosses performed to obtain homozygotes for three S-alleles. (b) Trait variation in S-locus homozygous individuals. (c) Trait variation in homozygous at the S-locus for the S-alleles Ah01 and Ah04 between families. (d) Effect of dominance on variation of phenotypic traits in S-locus homozygous individuals. (e) Number of phased haplotypes linked to S-alleles in each sample. (f) Effect of dominance on the accumulation of genetic load in S-flanking regions. (g) S-locus genotypes of individuals sequenced using the capture protocol. (h) S-locus genotypes of the offspring selected for haplotype phasing and the crosses for the study of phenotypic traits. (i) Effect of phytopathogen, phytophagous attacks and oxidative stress on the phenotypic traits. (j) Difference on the phenotypic traits variation between the two families for each allele tested.