Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date.
Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date.
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利用小麦叶尖和茎尖转录组分析揭示小麦抽穗期的分子机制和共表达基因。
DOI：
10.1186/s12864-021-07797-7
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发表时间：
2021-06-23
期刊：
影响因子：
4.4
通讯作者：
Kong X
中科院分区：
文献类型：
--
作者：
Yang Y;Zhang X;Wu L;Zhang L;Liu G;Xia C;Liu X;Kong X
小麦是世界上种植最广泛的作物之一。抽穗期是小麦环境适应性的重要指标，它不仅决定着小麦的开花期，而且决定着小麦的穗粒数。本研究选取早抽穗和晚抽穗回交后代的纯合基因型，分别在叶片和顶端分生组织的双棱期（W2. 0）和雌雄同株原基分化期（W3. 5）进行RNA-Seq分析。总共鉴定了18，352个差异表达基因（DEG），其中许多与小麦抽穗期基因密切相关。GO富集分析表明，糖代谢、海藻糖代谢、光合作用、光反应等与开花时间调控途径密切相关。基于MapMan代谢分析，DEG主要参与光反应、激素信号传导、脂质代谢、次级代谢和核苷酸合成。此外，还对45个转录因子基因家族注释了1，225个DEG，其中包括与开花时间密切相关的LFY、SBP和MADS盒转录因子。加权基因共表达网络分析（WGCNA）显示，与Vrn 1 - 5A、Vrn 3 - 7 B、Ppd-1D和WSOC 1有生物学联系的DEG分别为16、336、446和124个。TraesCS 2D 02 G181400编码MADS-MIKC转录因子，与Vrn 1 - 5A共表达，表明该基因可能与开花时间有关。RNA-Seq分析提供了小麦抽穗期关键花发育时期双棱分化期（W2.0）和雌雄同株原基分化期（W3.5）的转录组数据。在此基础上，构建了Vrn 1 - 5A、Vrn 3 - 7 B、WSOC 1和Ppd-1D中关键开花时间基因的共表达网络。此外，我们发现了一个潜在的候选开花时间基因TraesCS 2D 02 G181400。这些结果为进一步研究小麦抽穗期的调控机制奠定了基础。在线版本包含补充材料，可通过10.1186/s12864-021-07797-7获得。
Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date. The online version contains supplementary material available at 10.1186/s12864-021-07797-7.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
5.8
作者：
Orostica, Karen Y.;Verdugo, Ricardo A.
通讯作者：
Verdugo, Ricardo A.
影响因子：
4.5
作者：
Chen A;Dubcovsky J
通讯作者：
Dubcovsky J
agriGO：农业界的 GO 分析工具包
影响因子：
14.9
作者：
Du Z;Zhou X;Ling Y;Zhang Z;Su Z
通讯作者：
Su Z