IB-CAS  > 中科院植物分子生理学重点实验室
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
2019
Source PublicationFUNCTIONAL & INTEGRATIVE GENOMICS
ISSN1438-793X
Volume19Issue:6Pages:919-932
AbstractBread 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.
KeywordAlternative splicing Grain development Homoeologous gene Transcriptome Wheat
Subject AreaGenetics & Heredity
DOI10.1007/s10142-019-00693-0
Indexed BySCI
Language英语
WOS KeywordWHOLE-CHROMOSOME ANEUPLOIDY ; GENE-EXPRESSION ; ENDOSPERM DEVELOPMENT ; DYNAMIC CHANGES ; WHEAT EMBRYO ; SEED ; EVOLUTION ; PROTEOME ; REVEALS ; PROTEINS
WOS Research AreaGenetics & Heredity
WOS IDWOS:000490956700006
PublisherSPRINGER HEIDELBERG
SubtypeArticle
Publication PlaceHEIDELBERG
EISSN1438-7948
Funding OrganizationChinese 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 Emailyongxiu@ibcas.ac.cn
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/19824
Collection中科院植物分子生理学重点实验室
Affiliation1.[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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