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| Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq | |
Wei, Jun; Cao, Hong; Liu, Jing-dong; Zuo, Jing-hong; Fang, Yu4; Lin, Chih-Ta; Sun, Run-ze; Li, Wen-long; Liu, Yong-xiu
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| 2019 | |
| Source Publication | FUNCTIONAL & INTEGRATIVE GENOMICS
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| ISSN | 1438-793X |
| Volume | 19Issue:6Pages:919-932 |
| Abstract | Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat. |
| Keyword | Alternative splicing Grain development Homoeologous gene Transcriptome Wheat |
| Subject Area | Genetics & Heredity |
| DOI | 10.1007/s10142-019-00693-0 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | WHOLE-CHROMOSOME ANEUPLOIDY ; GENE-EXPRESSION ; ENDOSPERM DEVELOPMENT ; DYNAMIC CHANGES ; WHEAT EMBRYO ; SEED ; EVOLUTION ; PROTEOME ; REVEALS ; PROTEINS |
| WOS Research Area | Genetics & Heredity |
| WOS ID | WOS:000490956700006 |
| Publisher | SPRINGER HEIDELBERG |
| Subtype | Article |
| Publication Place | HEIDELBERG |
| EISSN | 1438-7948 |
| Funding Organization | Chinese Academy of SciencesChinese Academy of Sciences [XDA08010303] ; National Key Research and Development Program of China [2018YFD0100901] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31371242] |
| Corresponding Author Email | yongxiu@ibcas.ac.cn |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/19824 |
| Collection | 中科院植物分子生理学重点实验室 |
| Affiliation | 1.[Wei, Jun 2.Cao, Hong 3.Liu, Jing-dong 4.Zuo, Jing-hong 5.Fang, Yu 6.Li, Wen-long 7.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing 100093, Peoples R China 8.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China 9.[Lin, Chih-Ta 10.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 11.Sci & Technol Daily, Beijing 100093, Peoples R China |
| Recommended Citation GB/T 7714 | Wei, Jun,Cao, Hong,Liu, Jing-dong,et al. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq[J]. FUNCTIONAL & INTEGRATIVE GENOMICS,2019,19(6):919-932. |
| APA | Wei, Jun.,Cao, Hong.,Liu, Jing-dong.,Zuo, Jing-hong.,Fang, Yu.,...&Liu, Yong-xiu.(2019).Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq.FUNCTIONAL & INTEGRATIVE GENOMICS,19(6),919-932. |
| MLA | Wei, Jun,et al."Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq".FUNCTIONAL & INTEGRATIVE GENOMICS 19.6(2019):919-932. |
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| Wei-2019-Insights in（1878KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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