采用RNA-seq比较甘蓝型油菜矮化突变体与其高秆亲本的可变剪切  

Comparison of alternative splicing of Brassica napus dwarf mutant and its tall-stalked parents by using RNA-seq

作　　者：解艳芳 牛显飞 蒋学飞 刘双双 王茂林 

机构地区：[1]四川大学生命科学学院生物资源与生态环境教育部重点实验室

出　　处：《应用与环境生物学报》2018年第1期81-88,共8页Chinese Journal of Applied and Environmental Biology

基　　金：国家重点研发计划项目(2016YFD010020002);国家科技支撑计划项目(2013BAD01B03);“十三五”四川省作物育种攻关项目(16ZC2860)资助~~

摘　　要：为了研究甘蓝型油菜的矮化机制以及植物激素与矮化的关系,用Illumina Hiseq 4000平台对苗期甘蓝型油菜矮化突变体NDF-1及其高秆亲本3529的根进行RNA-seq测序.测序数据以甘蓝型油菜基因组作为参考基因组进行比对,用TopHat软件鉴定可变剪切,其中以3S和5S类型的可变剪切为主.对鉴定出的可变剪切基因做差异基因（DEGs）表达分析,共有913个DEGs,其中矮化突变体NDF-1相对于野生型3529上调的基因数有457个,显著下调的基因有456个.GO富集表明,发生可变剪切的差异基因主要功能是参与代谢过程和生物合成、细胞组分以及酶活性等过程.通过对代谢通路的富集,选取植物激素信号转导通路进行分析.该通路中的Bna Cnng57860D基因中存在两个仅发生在野生高秆3529油菜中的稳定性可变剪切,而基因BnaA05g32040D和BnaA03g50910D中发生的稳定性可变剪切仅在矮化突变体NDF-1中发现.本研究筛选出可能与油菜矮化相关的可变剪切,可为油菜矮化新品种培育研究奠定基础.Elucidating the causes of dwarfing in Brassica napus, especially the relationship between plant hormones and dwarfing, requires that the dwarf mutant of B. napus and its tall-stalked parents should be analyzed. We selected the roots of the B. napus dwarf mutant NDF-1 and its tall-stemmed parent 3529 at the seedling stage and conducted sequencing analysis by using the Illumina Hiseq 4000 platform. The resulting data were mapped with the sequenced B. napus genome as a reference. We identified and analyzed alternative splicing（AS） events for the transcriptome data by using software TopHat. The results showed that 3S and 5S were the main AS types. Next, the differentially expressed genes（DEGs） among the AS genes were identified. In all, 457 genes were significantly up-regulated and 456 genes were significantly down-regulated in the dwarf mutant NDF-1 relative to those in the wild-type 3529. The GO enrichment analysis indicated that the DEGs with AS were involved in functions such as metabolic and biosynthetic processes, cellular components, and enzymatic activity. Next, we used the KEGG pathway enrichment to analyze the dwarf-related metabolic pathway and plant hormone signal transduction pathway. Two stable AS events were found in Bna Cnng57860 D, which occurred only in the tall-stemmed parent 3529. Further, stable AS events in Bna A05g32040D and Bna A03g50910D were found only in the dwarf mutant NDF-1. By filtering AS events that might be related to dwarfing, we provide a new perspective for exploring the genetic regulation mechanism of B. napusdwarfing and lay the foundation for research on new varieties of dwarf rapeseed.

关 键 词：甘蓝型油菜 矮化突变体 RNA-SEQ 可变剪切 苗期根 

分 类 号：Q341[生物学—遗传学] S565.403[农业科学—作物学]