Functional & Integrative Genomics

, Volume 19, Issue 6, pp 919–932 | Cite as

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

  • Jun Wei
  • Hong Cao
  • Jing-dong Liu
  • Jing-hong Zuo
  • Yu Fang
  • Chih-Ta Lin
  • Run-ze Sun
  • Wen-long Li
  • Yong-xiu LiuEmail author
Original Article


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.


Alternative splicing Grain development Homoeologous gene Transcriptome Wheat 



We thank 1GENE Technologies Company for technology support (Hangzhou, China).

Author contributions

YXL designed the research. HC and JHZ performed embryo and endosperm collection and RNA extractions. JW and JDL performed the RNA-Seq analysis and data analysis. JW and YF performed the quantitative RT-PCR. JW and YXL wrote the manuscript. CTL, RZS, JDL, and WLL participated in the interpretation and discussion of results, and contributed to the writing of the paper.

Funding information

This work was financially supported by the Chinese Academy of Sciences grant (XDA08010303), the National Key Research and Development Program of China (2018YFD0100901), and the National Natural Science Foundation of China (31371242) to YL.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Key Laboratory of Plant Molecular Physiology, Institute of BotanyChinese Academy of SciencesBeijingChina
  2. 2.College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
  3. 3.Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
  4. 4.Science and Technology DailyBeijingChina

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