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

CORC > 植物研究所 > 中国科学院植物研究所 > 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, Yu 5; Lin, Chih-Ta ; Sun, Run-ze ; Li, Wen-long ; Liu, Yong-xiu
刊名	FUNCTIONAL & INTEGRATIVE GENOMICS
	2019
卷号	19 期号:6 页码:919-932
关键词	Alternative splicing Grain development Homoeologous gene Transcriptome Wheat
ISSN号	1438-793X
DOI	10.1007/s10142-019-00693-0
文献子类	Article
英文摘要	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.
学科主题	Genetics & Heredity
电子版国际标准刊号	1438-7948
出版地	HEIDELBERG
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
语种	英语
出版者	SPRINGER HEIDELBERG
WOS记录号	WOS:000490956700006
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]
内容类型	期刊论文
源URL	[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.Li, Wen-long 2.Cao, Hong 3.[Wei, Jun 4.Fang, Yu 5.Zuo, Jing-hong 6.Liu, Jing-dong 7.[Lin, Chih-Ta 8.Sci & Technol Daily, Beijing 100093, Peoples R China 9.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 10.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, 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.