An Wenyan, Gong Wenfang, He Shoupu, Pan Zhaoe, Sun Junling, Du Xiongming
State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430072, Hubei, China.
BMC Genomics. 2015 Oct 30;16:886. doi: 10.1186/s12864-015-2071-6.
Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum.
The stem apexes of wild-type upland cotton (Ari971) and its dwarf mutant (Ari1327) and tall-culm mutant (Ari3697) at the fifth true leaf stage were extracted for RNA, respectively. Transcriptome and small RNA libraries were constructed and subjected to next generation sequencing.
The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which was consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and pectate-lyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation.
This comprehensive interaction of the transcriptome and miRNA at tall-culm and dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.
矮化棉花对风雨损害的抵抗力更强，产量稳定且有增加，也是培育适合机械采收品种的理想材料。为了揭示参与株高调控的转录本和miRNA网络，基于陆地棉矮化突变体Ari1327（A1）、高杆突变体Ari3697（A3）和野生型Ari971（A9）进行了转录组和小RNA测序。
分别提取野生型陆地棉（Ari971）及其矮化突变体（Ari1327）和高杆突变体（Ari3697）在第五片真叶期的茎尖用于RNA提取。构建转录组和小RNA文库并进行下一代测序。
转录组测序分析表明，在A1 - A9和A3 - A9中，差异表达基因（DEG）排名前3的富集途径均归类为类胡萝卜素生物合成、植物 - 病原体相互作用和植物激素信号转导。ABA和IAA相关因子在突变体中差异表达。重要的是，我们发现SAUR表达下调，GH3表达上调，以及与ABA相关的基因如NCED和PP2C可能与Ari1327中株高生长受抑制有关，这与该突变体中较高的生长素和ABA含量一致。此外，靶向生长素响应因子（ARF）的miRNA160和靶向ABA响应元件结合因子的miRNA166（gma - miR166u和gma - miR166h - 3p）与棉花中的突变有关。我们注意到，细胞生长相关因子（gra - miR482靶向的smg7和6个新的miRNA以及osa - miR159f靶向的果胶裂解酶）、氧化还原反应相关因子（miR172靶向的细胞色素P450）以及miR828、miR858和miR159靶向的MYB基因也参与了棉花突变体的株高调控。共获得了代表32个已知miRNA家族的226个保守miRNA，并鉴定出对应23个独特RNA序列的38个新miRNA。共获得211个保守miRNA的531个靶标。使用PAREsnip，分别在A1 - A9和A3 - A9中验证了27和29个miRNA/靶标保守相互作用。此外，miRNA考证在A1 - A9中上调但在A3 - A9中下调，而miRNA159表现出相反的调控。
高杆和矮化突变体中转录组和miRNA的这种全面相互作用导致了株高调控机制的发现。它也为深入分析矮化突变基因以进一步培育矮化棉花提供了基础。
