Analysis of Transposable Element Associated Epigenetic Regulation under Drought in Maize
[Objective]Drought is one of the serious abiotic stresses influencing maize production worldwide.Understanding the molecular mechanisms underlying drought tolerance is of great importance in maize improvement.[Method]In the present study,representative maize inbred lines were selected for field drought experiment and the drought tolerance was estimated based on leaf relative water content and anthesis-silking interval.Two inbred lines with contrasting drought tolerance was used for genome resequencing and transposable element insertions were identified.The DNA methylation level of leaf and root tissues under different water treatments of the two lines were measured using Whole Genome Bisulfite Sequencing(WGBS).And the gene expression profiles of these samples were detected by RNA sequencing.The integrative atlas of transposable element insertion/deletion variants,differentially methylated regions and differentially expressed genes in the two lines were constructed.In addition,the transposable element insertion/deletion variant mediated epigenetic regulation of ZCN7,which has been conferred the drought tolerance function in our previous study,was analyzed.[Result]The field experiment showed inbred line H082183 showed highest drought tolerance,in which the leaf relative water content and anthesis-silking interval had no significant difference between drought and well-watered treatments.While the Lü28 displayed lowest leaf relative water content and largest anthesis-silking interval under drought.Thus,these two lines were selected for further analysis.A total of 333 754 and 333 296 transposable element insertions were identified in the genome of H082183 and Lü28,respectively.And 89 954 transposable element insertions were polymorphism between two lines.The transposable element insertions,introns and promoters showed higher CG and CHG methylation level than exons and untranslated regions.Furthermore,41 352 differentially methylated regions were identified between H082183 and Lü28.And 60%of the differentially methylated regions were located in the transposable element insertion\deletion variants and 5 kb flanking regions.The gene expression level showed negatively correlated with CG and CHG methylation.Differentially expression analysis between H082183 and Lü28 obtained 4 196 and 3 500 differentially expressed genes in leaf and root under drought,respectively.The 19.5%and 19.7%of these differentially expressed genes were located in differentially methylated regions.Three LTR transposable element insertions were identified in the 34 kb region of ZCN7 in Lü28 but absent in the genome H082183.And the DNA methylation levels of CG and CHG in this genomic region were significantly higher in Lü28 than H082183 under both drought and well-watered environments,which conferred higher ZCN7 expression in the drought tolerant line H082183.[Conclusion]Our results highlight the important role of interplay of transposable element insertions,DNA methylation and gene expression under drought.And gene expression regulation mechanism of ZCN7 relied on the transposable element insertion/deletion variants mediated DNA methylation was proposed.
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