Transcriptome Analysis Of Differentially Expressed Genes By RNA-Seq In A Dwarf Soybean Mutant

Plant height is an important agronomic character, and plays a profound effect on crop yield based on thestudy of crops, such as wheat, corn and rice. Improving plant heigt and genetic breeding applying dwarfgenes play key roles in enhancing production of staples. The latest studies showed that dwarfismmechanism was exclusively complicated. The studies of dwarf genes indicated that they were divided intotwo parts: qualitative trait gene controlled by a major gene and quantitative character genes cotrolled bypolygenes. Based on the study of phytohormone, the dwarf mutant was closely related to gibberellin (GA)and Brassinosteroids (BRs), and some dwarf mutations were associated with auxin (IAA).Object: The dwarf soybean mutant and wild type were used to analyze differentially expressed genes andexplore the dwarfism mechanism by RNA-Seq.Methods: The transcriptome were analyzed between dwarf soybean mutant and wild type by RNA-Seq.Quantitative Real-time RT-PCR (qRT-PCR) and semi-quantitative RT-PCR were used to detect theexpression profiles of differential expression genes. The differentially expressed genes that leaded to thedwarf phenotype could be predicted by gene functional annotation and bioinformatics.Results:(1) In this study, dwarf soybean mutants could be partially restored the wild phenotype byapplying GA3.(2)263M reads were obtained by RNA-Seq. The results showed that there were408up-regulated genes and256down-regulated genes in the root of dwarf soybean mutant, and1438up-regulated genes and1619down-regulated genes in the cotyledon of dwarf soybean mutant. According tothe above conclusion, there were129differentially expressed genes in the root and cotyledon,52geneswere up-regulated and77genes were down-regulated.(3) Many differentially expressed genes are relatedto phytohormone, in which Glyma19g01590gene related to GA3. Bioinformatics analysis indicated thatGlyma19g01590gene contained594bp open reading frame (ORF) and presumably encoded197aminoacids. Glyma19g01590protein contained a GASA (Gibberellic Acid-Stimulated in Arabidopsis) domainwhich could be regulated by GA3. In addition, semi-quantitative RT-PCR experiment showed that theexpression level of Glyma19g01590gene in mutant was higher than that in wild type. qRT-PCR resultshowed the expression quantity of Glyma19g01590gene in Gmdwarf1was24times in wild type.Conclusion: The results of RNA-Seq between dwarf soybean mutant and wild type showed that there were129differentially expressed genes in the root and cotyledon,52genes were up-regulated and77genes weredown-regulated. Glyma19g01590gene was one of differentially expressed genes and its expression relatedto GA, and Glyma19g01590protein contained a GASA domain that could be regulated by GA3. Theexpression level of Glyma19g01590gene in mutant was significantly higher than wild type. In addition,dwarf soybean mutants could be partially restored the wild phenotype by applying GA3. The resultsindicated that Glyma19g01590gene was perhaps one of the genes that were responsible for dwarfphenotype.