Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq
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.
KeywordsAlternative splicing Grain development Homoeologous gene Transcriptome Wheat
We thank 1GENE Technologies Company for technology support (Hangzhou, China).
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.
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.
- Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357:93–97. https://doi.org/10.1126/science.aan0032 CrossRefPubMedGoogle Scholar
- Bottley A, Koebner RMD (2008) Variation for homoeologous gene silencing in hexaploid wheat. Plant J, 56: 297–302. doi:18564382Google Scholar
- Bottley A, Chapman NH, Koebner RMD. (2008) Homoeologous gene silencing in tissue cultured wheat callus. BMC Genet, 9: 65. doi:18928533Google Scholar
- Brinton J, Simmonds J, Uauy C (2018) Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat. BMC Plant Biol, 18: 22. doi:29370763Google Scholar
- Cao H, He M, Zhu C, Yuan L, Dong L, Bian Y, Zhang W, Yan Y (2016) Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D-DIGE-based integrative proteome analysis. Proteomics, 16: 1515–1536. doi:26968330Google Scholar
- Drisch RC, Stahl Y (2015) Function and regulation of transcription factors involved in root apical meristem and stem cell maintenance. Front Plant Sci, 6: 505. doi: https://doi.org/10.3389/fpls.2015.00505
- Fábián A, Jäger K, Rakszegi M, Barnabás B (2011) Embryo and endosperm development in wheat (Triticum aestivum L.) kernels subjected to drought stress. Plant Cell Rep, 30: 551–563. doi:21246199Google Scholar
- Gao F, Wen W, Liu J, Rasheed A, Yin G, Xia X, Wu X, He Z (2015) Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the chinese wheat cross Zhou 8425B/Chinese Spring. Front Plant Sci, 6: 1099. doi: https://doi.org/10.3389/fpls.2015.01099
- Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y (2012) Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC Plant Biol, 12: 147. doi:22900893Google Scholar
- Han R, Jian C, Lv J, Yan Y, Chi Q, Li Z, Wang Q, Zhang J, Liu X, Zhao H (2014) Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics 15:289. https://doi.org/10.1186/1471-2164-15-289 CrossRefPubMedPubMedCentralGoogle Scholar
- Han C, Zhen S, Zhu G, Bian Y, Yan Y (2017) Comparative metabolome analysis of wheat embryo and endosperm reveals the dynamic changes of metabolites during seed germination. Plant Physiol Biochem, 115: 320–327. doi:28415032Google Scholar
- He M, Zhu C, Dong K, Zhang T, Cheng Z, Li J, Yan Y (2015) Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination. BMC Plant Biol 15:97. https://doi.org/10.1186/s12870-015-0471-z CrossRefPubMedPubMedCentralGoogle Scholar
- Li A, Liu D, Wu J, Zhao X, Hao M, Geng S, Yan J, Jiang X, Zhang L, Wu J, Yin L, Zhang R, Wu L, Zheng Y, Mao L (2014) mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell 26:1878–1900. https://doi.org/10.1105/tpc.114.124388 CrossRefPubMedPubMedCentralGoogle Scholar
- Liu MR et al (2015) Exogenous application of brassinolide ameliorates mowing stress in leymus chinensis (Trin.). Philipp Agric Sci 98:202–208Google Scholar
- Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498–502. https://doi.org/10.1038/nature24486 CrossRefPubMedGoogle Scholar
- Ma C, Zhou J, Chen G, Bian Y, Lv D, Li X, Wang Z, Yan Y (2014) iTRAQ-based quantitative proteome and phosphoprotein characterization reveals the central metabolism changes involved in wheat grain development. BMC Genomics, 15: 1029. doi:25427527Google Scholar
- Okada T, Jayasinghe JEARM, Nansamba M, Baes M, Warner P, Kouidri A, Correia D, Nguyen V, Whitford R, Baumann U (2018) Unfertilized ovary pushes wheat flower open for cross-pollination. J Exp Bot, 69: 399–412. doi:29202197Google Scholar
- Qi B, Huang W, Zhu B, Zhong X, Guo J, Zhao N, Xu C, Zhang H, Pang J, Han F, Liu B (2012) Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol 10:3. https://doi.org/10.1186/1741-7007-10-3 CrossRefPubMedPubMedCentralGoogle Scholar
- Sanyal SK, Kanwar P, Samtani H, Kaur K, Jha SK, Pandey GK (2017) Alternative splicing of CIPK3 results in distinct target selection to propagate ABA signaling in Arabidopsis. Front Plant Sci, 8: 1924. doi: https://doi.org/10.3389/fpls.2017.01924
- Tasleem-Tahir A, Nadaud I, Chambon C, Branlard G (2012) Expression profiling of starchy endosperm metabolic proteins at 21 stages of wheat grain development. J Proteome Res, 11: 2754–2773. doi:22394196Google Scholar
- Trapnell et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 7: 562–578. doi:22383036Google Scholar
- Wegel E, Shaw PJ (2005) Chromosome organization in wheat endosperm and embryo. Cytogenet Genome Res, 109: 175–180. doi:15753574Google Scholar
- Yu CW et al. (2015a) Structural development of wheat nutrient transfer tissues and their relationships with filial tissues development. Protoplasma, 252: 605–617. doi:25252888Google Scholar
- Yu X, Zhou L, Zhang J, Yu H, Xiong F, Wang Z (2015b) Comparison of starch granule development and physicochemical properties of starches in wheat pericarp and endosperm. J Sci Food Agric, 95: 148–157. doi:24740388Google Scholar
- Yuan XY, Zhang LG, Huang L, Yang HJ, Zhong YT, Ning N, Wen YY, Dong SQ, Song XE, Wang HF, Guo PY (2017) Spraying brassinolide improves sigma broad tolerance in foxtail millet (Setaria italica L.) through modulation of antioxidant activity and photosynthetic capacity. Sci Rep, 7: 11232. doi: https://doi.org/10.1038/s41598-017-11867-w
- Zhang H, Bian Y, Gou X, Zhu B, Xu C, Qi B, Li N, Rustgi S, Zhou H, Han F, Jiang J, von Wettstein D, Liu B (2013) Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. P Natl Acad Sci USA 110:3447–3452. https://doi.org/10.1073/pnas.1300153110 CrossRefGoogle Scholar
- Zhang M, Ma C-Y, Lv D-W, Zhen S-M, Li X-H, Yan Y-M (2014) Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions. J Rroteome Res, 13: 4281–4297. doi:25145454Google Scholar
- Zheng N, Schulman BA, Song L, Miller JJ, Jeffrey PD, Wang P, Chu C, Koepp DM, Elledge SJ, Pagano M, Conaway RC, Conaway JW, Harper JW, Pavletich NP (2002) Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex. Nature 416:703–709. https://doi.org/10.1038/416703a CrossRefPubMedGoogle Scholar
- Zhou X, Guo Y, Zhao P, M-x S (2018) Comparative analysis of WUSCHEL-related homeobox genes revealed their parent-of-origin and cell type-specific expression pattern during early embryogenesis in tobacco. Front Plant Sci 9:311. https://doi.org/10.3389/fpls.2018.00311 CrossRefPubMedPubMedCentralGoogle Scholar
- Zhu G, Li W, Zhang F, Guo W (2018) RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii. BMC Genomics, 19: 73. doi:29361913Google Scholar