The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and Arabidopsis lyrata
- Univ. Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, France
Figures
Figure 1 with 1 supplement
Effect of homozygosity at the S-locus on 13 phenotypic traits compared to heterozygotes.
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 …
Figure 1—figure supplement 1
Experimental protocol.
(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 …
Figure 2 with 8 supplements
Linkage to the S-locus locally distorts the phylogenetic relationships.
(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 …
Figure 2—figure supplement 1
Analysis of major components obtained for haplotypes of A. halleri of the Nivelle (black dots) and Mortagne (grey dots) populations based on SNPs in the first 5 kb, between 5 and 25 kb, and between 25 kb and 50 kb away from the S-locus.
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 …
Figure 2—figure supplement 2
Analysis of major components (AMC) obtained for haplotypes of A. lyrata (of the PIN: grey dots, IND: red dots; and TSS: blue dots) populations based on the SNPs in the first 5 kb, between 5 and 25 kb, and between 25 kb and 50 kb away from the S-locus.
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 …
Figure 2—figure supplement 3
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. halleri (populations Nivelle and Mortagne) across the first 25 kb flanking the S-locus.
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 …
Figure 2—figure supplement 4
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. halleri (populations Nivelle and Mortagne) based on the nucleotide positions between 25 kb and 50 kb away from the S-locus.
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 …
Figure 2—figure supplement 5
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. lyrata (populations PIN, IND, TSS) across the first 5 kb flanking the S-locus.
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 …
Figure 2—figure supplement 6
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. lyrata (populations PIN, IND, TSS) based on the nucleotide positions between 5 kb and 10 kb away from the S-locus.
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 …
Figure 2—figure supplement 7
The genetic structure of SNPs in the S-locus flanking regions in A. halleri and A. lyrata.
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 …
Figure 2—figure supplement 8
Patterns of genetic associations between S-alleles and SNPs across the genome.
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 …
Figure 3
No overall effect of S-allele dominance on the total number of zerofold degenerate mutations (S0f) in the linked genomic regions within 25 kb.
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 …
Figure 4
The number of zerofold degenerate mutations fixed in the 25 kb regions flanking the S-locus increases with dominance of the S-allele associated.
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 …
Figure 5
Stochastic simulations confirm the contrasted architecture of the load of deleterious mutations linked to dominant vs. recessive S-alleles.
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…
Tables
Table 1
Proportion of S-locus homozygous offspring having reached the reproductive stage for three different S-alleles.
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 |
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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.
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*
p-Values were obtained after 10,000 random permutations, respectively.
Additional files
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Supplementary file 1
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.
- https://cdn.elifesciences.org/articles/94972/elife-94972-supp1-v1.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/94972/elife-94972-mdarchecklist1-v1.docx
