Association Analysis Of Long Non-coding RNAs And Inportant Agronomic Traits In Maize

Long non-coding RNA(lncRNA)is emerging as a class of regulatory factors that play important roles in various biological processes.The long intergenic non-coding RNA(lincRNA)is a group of lncRNAs located in intergenic regions,the function of which in plants(especially in crops)is still limited.Maize(Zea mays.L),a major economic crop,is widely used and of great economic value.In addition,the genome of maize is complex.With the constant updating of genome annotation information,lncRNA research has gradually gained attention.It was found that lncRNA may play an important regulatory role in maize growth and development.In this thesis,an integrative bioinformatics analysis was performed for the identification,characterization and functional annotation of lincRNAs in maize.The main results are as follows:1.A new bioinformatics pipeline has been developed for the identification of lincRNA at the genome-scale.Through assembling 145 transcriptome data and integrating published lncRNA datasets,total of 3,292 maize lincRNAs with high confidence have been identified.2.Compared with mRNAs,lincRNAs were shorter,and had lower expression level.Besides,the expression of lincRNA was coincident with the expression of adjoining coding genes.Moreover,446 position-conserved maize lincRNAs were obtained through alignment with the lincRNAs of Arabidopsis thaliana,rice and soybean.3.Co-expression analysis revealed that lincRNAs were involved in important biological processes including flower development,chloroplast photosynthesis and stress response,and coexpressed with bHLH,NAC,C2H2,MYB,WRKY and other transcription factor family genes.4.GWAS analysis identified eight SNPs significantly associated with agronomic traits such as tassel branch number and ear leaf length,and those SNPs were associated with 16 lincRNAs in total.