Molecular Mechanism For Enhanced Salinity Tolerance Of Tetraploid Rice Regulated By DNA Methylation

Polyploidy is a prominent feature for genome evolution in all flowering plants.Many plants including crops like wheat,cotton and potato are polyploids.Although some crops are known as diploid,like rice,maize and soybean,they are derived from at least one round of ancient whole-genome duplication followed by diploidization.The common occurrence of polyploidy suggests an evolutionary potential.Polyploids often show enhanced fitness in diverse and extreme environments.Polyploidization can stimulate transcriptional and epigenetic changes,however their roles in enhanced fitness of polyploids remained elusive.Soil salinity affects more than 6%land area in the world and is a threat for agriculture and production of crops.In this study,we analyzed transcriptomes and single-base-resolution methylomes in diploid and autotetraploid rice under control and salinity condition to understand the epigenetic mechanism of enchanced fitness in tetraploid rice.1.Under salinity condition,tetraploid rice(02428)exhibited better growth and higher survival rates than diploid rice.Both fresh and dry weights in shoots or roots were reduced to a great extent in diploid than in tetraploid rice.After salt stress for 2 and 4 days,tetraploid rice had a lower Na~+uptake and a higher K~+/Na~+raito than diploid rice in both shoots and roots,however,the total K~+content was similar between diploid and tetraploid rice under salinity stress.2.After salt stress,more genes were differentially expressed and showed higher expression-level changes in tetraploid(3,228 upregulated genes and 3,524 downregulated genes)than in diploid rice(2,448 upregulated genes and 2,833 downregulated genes),suggesting that polyploidy reprogramed genes expression upon salt stress.Interestingly,many JA(jasmonate acid)-related genes were induced in tetraploid rice at significantly higher levels under salt stress.And the stronger activation of JA-related genes in tetraploid rice occured in early phase of salt stress.Consistent with our RNA-seq data,JA-Ile(Jasmonoyl isoleucine)content was increased in both but more in tetraploid than in diploid rice after salt stress for three hours.Also,tetraploid rice showed a greater response of JA signaling than diploid rice.The data suggest that the JA pathways are strongly activated in tetraploid rice,contributing to increased salt stress tolerance.3.DNA methylation changes induced by polyploidy and salt stress mainly occurred in CHH contexts.After polyploidization,TEs were repressed,which may induce CHH hypomethylation(8645 hypo-DMRs)in tetraploid rice.Upon salt stress,TEs were derepressed in tetraploid rice,leading to CHH methylation increases(6535 hyper-DMRs).In diploid rice,TEs expression and CHH methylation levels remained unchanged after salt stress.Interestingly,differentially methylated regions(DMRs)induced by polyploidization and salt stress occurred in TEs(transposable elements)adjacent to stress-related genes,like JA biosynthesis and signaling related genes.After salt stress,hypomethylation in tetraploid rice potentiated stress-related genes including JA biosynthesis and signaling related genes for more rapid and stronger activation.In turn,elevated expression of stress-responsive genes in tetraploid rice can induce hypermetylation and suppress proximal TEs.The dual roles of polyploidy-induced hypomethylation in rapid and strong stress response and stress-induced hypermethylation to repress proximal TEs may provide an advantage for enhanced salt tolerance of tetraploid rice.4.After stress removal,CHH hypomethylated status of tetraploid rice prior to the initial salt treatment were partly retained,including genomic regions adjacent to JA-related genes.After the second round of salt stress,these regions became hypermethylated in tetraploid rice.Consistent with gene expression changes after the first salt treatment,JA-related genes were stronger activated in tetraploid rice after the second round of salt stress,contributing enhanced salinity tolerance.5.Furthermore,we found JA-related genes were also expressed at higher levels in Nipponbare tetraploid than in diploid after salt stress.As a result,Nipponbare tetraploid showed higher survival rates than diploid under salinity condition.Polyploidy-induced hypomethylation regulated similar loci(2014 genes)between Nipponbare and 02428,including JA pathway genes.Together,these data indicate a shared mechanism for ploidy-induced CHH hypomethylation to prime a more rapid and stronger activation of JA-related genes in response to salt stress in two rice tetraploids than in diploids.