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萝卜(Raphanus sativus L.)主根转录组分析揭示主根增粗过程中的复杂调控网络。

Transcriptome Profiling of Taproot Reveals Complex Regulatory Networks during Taproot Thickening in Radish (Raphanus sativus L.).

作者信息

Yu Rugang, Wang Jing, Xu Liang, Wang Yan, Wang Ronghua, Zhu Xianwen, Sun Xiaochuan, Luo Xiaobo, Xie Yang, Everlyne Muleke, Liu Liwang

机构信息

National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China; School of Life Science, Huaibei Normal UniversityHuaibei, China.

National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University Nanjing, China.

出版信息

Front Plant Sci. 2016 Aug 22;7:1210. doi: 10.3389/fpls.2016.01210. eCollection 2016.

Abstract

Radish (Raphanus sativus L.) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish taproot thickening process and explore the molecular mechanism underlying taproot development, three cDNA libraries from radish taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2), and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes, respectively. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325, and 7392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR, and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with taproot thickening in radish was put forward. The taproot formation of radish is mainly attributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism processes. These results could provide new insights into the complex molecular mechanism underlying taproot thickening and facilitate genetic improvement of taproot in radish.

摘要

萝卜(Raphanus sativus L.)是全球最重要的蔬菜作物之一。主根加粗是萝卜生命周期中决定产量和品质的关键发育时期。为了分离参与萝卜主根加粗过程的差异表达基因(DGE)并探索主根发育的分子机制,利用RNA-Seq技术构建并测序了来自萝卜主根在皮层分裂前期(L1)、皮层分裂期(L2)和膨大期(L3)采集的三个cDNA文库。从这三个文库中获得了超过七百万条clean reads,其中分别有4,717,617条(L1,65.35%)、4,809,588条(L2,68.24%)和4,973,745条(L3,69.45%)reads与萝卜参考基因匹配。三个文库共产生了85,939条转录本,其中在L1与L2、L1与L3以及L2与L3的比较中分别检测到10,450、12,325和7392条差异表达转录本(DET)。基因本体论和通路分析表明,许多差异表达基因,包括EXPA9、细胞周期蛋白、钙调蛋白、 syntaxin、MADS-box、SAUR和CalS,参与了细胞事件、细胞壁修饰、植物激素水平调节、信号转导和代谢,这可能与主根加粗有关。此外,mRNA-miRNA的综合分析表明,43个miRNA和92个基因形成了114个miRNA-靶标mRNA对共表达,并从不同文库构建了三个主根的miRNA-靶标调控网络。最后,使用RT-qPCR分析证实了16个选定基因的表达模式。提出了一个与萝卜主根加粗相关的遗传调控网络的假设模型。萝卜主根的形成主要归因于细胞分化、分裂和扩展,这受到某些特定信号转导途径和代谢过程的调节和促进。这些结果可以为萝卜主根加粗的复杂分子机制提供新的见解,并有助于萝卜主根的遗传改良。

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