Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq

doi:10.1007/s10142-019-00693-0

	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, Yu 4; Lin, Chih-Ta ; Sun, Run-ze ; Li, Wen-long ; Liu, Yong-xiu
	2019
发表期刊	FUNCTIONAL & INTEGRATIVE GENOMICS
ISSN	1438-793X
卷号	19 期号:6 页码:919-932
摘要	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.
关键词	Alternative splicing Grain development Homoeologous gene Transcriptome Wheat
学科领域	Genetics & Heredity
DOI	10.1007/s10142-019-00693-0
收录类别	SCI
语种	英语
WOS关键词	WHOLE-CHROMOSOME ANEUPLOIDY ; GENE-EXPRESSION ; ENDOSPERM DEVELOPMENT ; DYNAMIC CHANGES ; WHEAT EMBRYO ; SEED ; EVOLUTION ; PROTEOME ; REVEALS ; PROTEINS
WOS研究方向	Genetics & Heredity
WOS记录号	WOS:000490956700006
出版者	SPRINGER HEIDELBERG
文献子类	Article
出版地	HEIDELBERG
EISSN	1438-7948
资助机构	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]
作者邮箱	yongxiu@ibcas.ac.cn
引用统计	被引频次：9[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/19824
专题	中科院植物分子生理学重点实验室
作者单位	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
推荐引用方式 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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