Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana

Relating molecular variation to phenotypic diversity is a central goal in evolutionary biology. In Arabidopsis thaliana, FLOWERING LOCUS C (FLC) is a major determinant of variation in vernalization—the acceleration of flowering by prolonged cold. Here, through analysis of 1307 A. thaliana accessions, we identify five predominant FLC haplotypes defined by noncoding sequence variation. Genetic and transgenic experiments show that they are functionally distinct, varying in FLC expression level and rate of epigenetic silencing. Allelic heterogeneity at this single locus accounts for a large proportion of natural variation in vernalization that contributes to adaptation of A. thaliana

The maternal environment interacts with genetic variation in regulating seed dormancy in Swedish Arabidopsis thaliana.

Seed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could presumably account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions

The effect of seed maturation temperature on germination trajectories.

<p>Clustering dendrogram reporting the high disparity in germination trajectories across maternal environments (warm or cold) and time (21, 63 or 105 days of after-ripening). The six major clusters are numbered from 1 to 6 and are indicated with colored circles on the nodes of the dendrogram. Lines names are colored according to latitude of origin: south Sweden (red) is defined as the region below 60°N and north Sweden (blue) as the region above 60°N. Heatmap colors represent germination phenotypes, with darker shades indicating higher germination rates.</p

The geographic pattern of the dormancy variation.

<p>Correlation between latitude and either (A) GR21 warm or (B) GR21 cold. As in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190242#pone.0190242.g002" target="_blank">Fig 2</a>, we define south Sweden (S) as the region below 60°N and north Sweden (N) as the region above 60°N. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190242#pone.0190242.s001" target="_blank">S1 Fig</a> for the correlations between latitude and the other dormancy phenotypes.</p

GWAS for seed dormancy traits.

<p>Manhattan plots of genome-wide association results for germination rate of seeds set either in (A-C) warm or (D-F) cold environments and after-ripened for (A and D) 21, (B and E) 63 or (C and F) 105 days. The dotted horizontal line indicates a significance level of 0.05 after Bonferroni correction for multiple testing. Triangles show the position of the nine peaks with <i>P</i> values < 10^-6 for at least one phenotype. Triangle color indicates the type of effect: white, ‘common’; black, ‘specific’; grey, ‘unclear’. Are only displayed SNPs with a minor allele frequency ≥ 14%. The GWAS results are fully browsable online: <a href="https://goo.gl/dt53nc" target="_blank">https://goo.gl/dt53nc</a>.</p

Heritability of seed dormancy traits.

<p>Heritability of seed dormancy traits.</p

The effect of seed maturation temperature on seed dormancy variation.

<p>Scatter plots and histograms showing the relationship between dormancy traits as well as their phenotypic distribution. Seeds were produced either under warm (21°C; red) or cold (15°C; blue) conditions and after-ripened for either (A) 21, (B) 63 or (C) 105 days. Error bars represent the standard deviation within genotypes (n = 3, in few cases n = 2).</p

SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1

Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1

Methylation analysis at <i>BONSAI</i> in <i>sg1-1.</i>

<p>(A) Methylation in the three cytosine contexts near <i>BNS</i>. The spreading of DNA methylation from the adjacent LINE element (At1g73175) is visible in <i>sg1-1</i>. (B) Histone H3K9me2 accumulation in <i>BNS</i> determined by ChIP analyses. The correspondence of genomic regions tested by ChIP is shown on a gene schematic based on TAIR v10. Error bars are SEM from at least three biological replicates.</p