Transcriptome Analysis Of Maize Seedling Under Waterlogging Stress And Cloning Of Candidate Gene For Waterlogging Tolerance

Waterlogging, an abiotic stress, seriously restricts maize production and productivity in tropical and subtropical regions around the world. Unraveling the genetic basis of waterlogging tolerance in maize seedling is of great importance for guiding genetic improvement of maize waterlogging tolerance. Recent studies show that waterlogging tolerance of maize seedlings is a complex quantitative trait that is controlled by polygenes. Our previous study identified a major QTL for waterlogging tolerance in5.04bin by Genome Wide Association Study (GWAS) and linkage mapping.Using the material of two corn recombinant inbred sister lines A3237(tolerance) and A3239(sensitive), the aims of this study is screening and cloning important candidate gene for waterlogging tolerance and promoter sequence, analysis of gene structure and expression patterns in different materials, waterlogging periods (0h,2h,4h,8h and12h) and tissues, combining simplified genome sequencing, QTL mapping, RNA-seq technology and bioinformatics methods.The main conclusions of this study are as follows:(1) To determine differential genes expression selected by multiple greater than2-fold difference in expression and P value less than0.05as threshold value, there were608differentially expressed genes in seedlings of A3237and A3239under waterlogging stress. GO annotation found differentially expressed genes mainly involved in the biosynthesis of metabolic activity, oxidoreductase activity, stress responses, and most genes were high expression in inbred line A3237(waterlogging tolerance).(2)25candidate genes for waterlogging tolerance were found in5.04bin, combining gene expression, QTL mapping and bioinformatics methods. Only the coding region of GM2and GM17were difference in A3237and A3239, wherein the sequences of two genes transcript in A3239were consistent with reference B73gene sequence. Relative to the gene sequence of A3239, the gene sequence of A3237existed a mutation in GM2, leading alanine to threonine, and a missing66bp sequence transcripts in GM17. (3) GM2was a gene coding for protein with typically AP2domain, and GM17was a gene encoding a protein of HLH double helix domain. Real-time PCR analyses showed that GM2and GM17gene expression were rapid induced by waterlogging stress. There were significant differences in the amount of GM2expression between A3237and A3239. There were no significant differences in the amount of GM17expression between A3237and A3239.(4) The gene promoter region of GM2and GM17contained multiple cis-regulatory elements related anaerobic response, such as ARE, G-box, GC-motif, MYB motif. The downstream gene expression might be induced by waterlogging stress. In GM2gene promoter region upstream, there was a910bp insertion/deletion between A3237and A3239, determined by a natural gypsy class retrotransposon insertion mutation.The retrotransposon insertion might be upregulated its expression level and the molecular markers for insertion/deletion might be used in molecular breeding of maize waterlogging tolerance.Our results may be meaningful for illustrating the function, genetic effects and molecular mechanisms of major QTL for waterlogging tolerance in5.04bin, and provide a theoretical basis and gene resources for breeding new waterlogging tolerance of maize varieties.