Epigenetic regulation of autonomous pathway mediates polymorphism of flowering time in Arabidopsis

<p><span>Plant flowering time is affected by endogenous and exogenous factors, but its polymorphism among different populations of a species has not been fully explained yet. Here, 27 <em>Arabidopsis thaliana</em> populations were used to </span><span>determine</span><span> how autonomous pathway gene methylation affects flowering differences </span><span>by</span><span> regulating gene expression patterns. DNA methylation analysis, qPCR and transgenic verification</span> <span>showed that polymorphism in the flowering time among the <em>Arabidopsis</em> populations ranged from 19 to 55 days was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway</span><span>,</span><span> <em>FVE</em>, <em>FY</em>, <em>FLD</em>, <em>PEP</em>, <em>HDA5</em> and <em>PPR</em> <em>39-1</em> and</span><span> their </span><span>relative expression levels</span> <span>(P &lt; 0.05). Expression of selected <em>FVE</em> and <em>FVE(CS) </em>separately</span> <span>through codon degeneracy substitution of cytosine led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of </span><span>methylated sites</span><span> of <em>FVE</em> and <em>FVE(CS)</em> among those transgenic plants and recipient Col-0 verified the close relationship between their methylation number, expression and the flowering times. Our findings firstly suggest that the methylation variation of those six key upstream transcription factors regulates</span><span> the</span><span> gene expression level of </span><span>the</span><span> autonomous pathway, leading to phenotypic differences in flowering time of Arabidopsis. </span><span>The</span><span> <em>FVE(CS)</em></span><span> and <em>FVE</em> genes in transgenic plants tend to be hypermethylated, and this could be a protective mechanism for plants. However, modification of gene sequence through codon degeneracy substitution to reduce cytosine can avoid hypermethylated transferred-genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology.</span></p>