Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI, Zhihui WU, Yufeng ZHANG, Dandan GUO, Yuzhou XU, Weixia CHEN, Haiying ZHOU, Mingshan YOU, Baoyun LI

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Front. Agr. Sci. Eng. ›› 2014, Vol. 1 ›› Issue (3) : 214-222. DOI: 10.15302/J-FASE-2014024
RESEARCH ARTICLE
RESEARCH ARTICLE

Transcriptome analysis of wheat grain using RNA-Seq

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Abstract

With the increase in consumer demand, wheat grain quality improvement has become a focus in China and worldwide. Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. In this study, two cDNA libraries from the developing grain and leaf-stem components of bread wheat cultivar, Nongda211, were sequenced using Roche/454 technology. There were 1061274 and 1516564 clean reads generated from grain and leaf-stem, respectively. A total of 61393 high-quality unigenes were obtained with an average length of 1456 bp after de novo assembly. The analysis of the 61393 unigenes involved in the biological processes of the grain showed that there were 7355 differentially expressed genes upregulated in the grain library. Gene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that many transcription products and transcription factors associated with carbohydrate and protein metabolism were abundantly expressed in the grain. These results contribute to excavate genes associated with wheat quality and further study how they interact.

Keywords

transcriptome analysis / wheat grain / differentially expressed genes / enrichment analysis

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Liu WEI, Zhihui WU, Yufeng ZHANG, Dandan GUO, Yuzhou XU, Weixia CHEN, Haiying ZHOU, Mingshan YOU, Baoyun LI. Transcriptome analysis of wheat grain using RNA-Seq. Front. Agr. Sci. Eng., 2014, 1(3): 214‒222 https://doi.org/10.15302/J-FASE-2014024

References

[1]
Gupta P K, Mir R R, Mohan A, Kumar J. Wheat genomics: present status and future prospects. International Journal of Plant Genomics, 2008, 2008: 1-36
CrossRef Pubmed Google scholar
[2]
Evers T, Millar S. Cereal grain structure and development: some implications for quality. Journal of Cereal Science, 2002, 36(3): 261-284
CrossRef Google scholar
[3]
Laudencia-Chingcuanco D L, Stamova B S, Lazo G R, Cui X, Anderson O D. Analysis of the wheat endosperm transcriptome. Journal of Applied Genetics, 2006, 47(4): 287-302
CrossRef Pubmed Google scholar
[4]
Hammond-Kosack M C U, Holdsworth M J, Bevan M W. In vivo footprinting of a low molecular weight glutenin gene (LMWG-1D1) in wheat endosperm. The EMBO Journal, 1993, 12(2): 545-554
Pubmed
[5]
Shewry P R, Halford N G. Cereal seed storage proteins: structures, properties and role in grain utilization. Journal of Experimental Botany, 2002, 53(370): 947-958
CrossRef Pubmed Google scholar
[6]
Ball S G, Morell M K. From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. Annual Review of Plant Biology, 2003, 54(1): 207-233
CrossRef Pubmed Google scholar
[7]
Hattori J, Ouellet T, Tinker N A. Wheat EST sequence assembly facilitates comparison of gene contents among plant species and discovery of novel genes. Genome, 2005, 48(2): 197-206
CrossRef Pubmed Google scholar
[8]
Leader D J. Transcriptional analysis and functional genomics in wheat. Journal of Cereal Science, 2005, 41(2): 149-163
CrossRef Google scholar
[9]
McIntosh S, Watson L, Bundock P, Crawford A, White J, Cordeiro G, Barbary D, Rooke L, Henry R. SAGE of the developing wheat caryopsis. Plant Biotechnology Journal, 2007, 5(1): 69-83
CrossRef Pubmed Google scholar
[10]
Wan Y, Poole R L, Huttly A K, Toscano-Underwood C, Feeney K, Welham S, Gooding M J, Mills C, Edwards K J, Shewry P R, Mitchell R A. Transcriptome analysis of grain development in hexaploid wheat. BMC Genomics, 2008, 9(1): 121-136
CrossRef Pubmed Google scholar
[11]
Yang X, Xu H, Li W, Li L, Sun J, Li Y, Yan Y, Hu Y. Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat. BMC Genomics, 2011, 12(1): 513-524
CrossRef Pubmed Google scholar
[12]
Xu H, Gao Y, Wang J. Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PLoS ONE, 2012, 7(2): e30646
CrossRef Pubmed Google scholar
[13]
Margulies M, Egholm M, Altman W E, Attiya S, Bader J S, Bemben L A, Berka J, Braverman M S, Chen Y J, Chen Z, Dewell S B, Du L, Fierro J M, Gomes X V, Godwin B C, He W, Helgesen S, Ho C H, Irzyk G P, Jando S C, Alenquer M L, Jarvie T P, Jirage K B, Kim J B, Knight J R, Lanza J R, Leamon J H, Lefkowitz S M, Lei M, Li J, Lohman K L, Lu H, Makhijani V B, McDade K E, McKenna M P, Myers E W, Nickerson E, Nobile J R, Plant R, Puc B P, Ronan M T, Roth G T, Sarkis G J, Simons J F, Simpson J W, Srinivasan M, Tartaro K R, Tomasz A, Vogt K A, Volkmer G A, Wang S H, Wang Y, Weiner M P, Yu P, Begley R F, Rothberg J M. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437(7057): 376-380
Pubmed
[14]
Mardis E R. The impact of next-generation sequencing technology on genetics. Trends in Genetics, 2008, 24(3): 133-141
CrossRef Pubmed Google scholar
[15]
Vera J C, Wheat C W, Fescemyer H W, Frilander M J, Crawford D L, Hanski I, Marden J H. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 2008, 17(7): 1636-1647
CrossRef Pubmed Google scholar
[16]
Altschul S F, Madden T L, Schäffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997, 25(17): 3389-3402
CrossRef Pubmed Google scholar
[17]
Finn R D, Mistry J, Tate J, Coggill P, Heger A, Pollington J E, Gavin O L, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer E L, Eddy S R, Bateman A. The Pfam protein families database. Nucleic Acids Research, 2010, 38(Suppl 1): D211-D222
CrossRef Pubmed Google scholar
[18]
Götz S, García-Gómez J M, Terol J, Williams T D, Nagaraj S H, Nueda M J, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 2008, 36(10): 3420-3435
CrossRef Pubmed Google scholar
[19]
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 2008, 36(Database issue): D480-D484
Pubmed
[20]
Li B, Dewey C N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 2011, 12(1): 323-338
CrossRef Pubmed Google scholar
[21]
Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008, 5(7): 621-628
CrossRef Pubmed Google scholar
[22]
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology, 2010, 11(10): R106
CrossRef Pubmed Google scholar
[23]
Wang L, Feng Z, Wang X, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 2010, 26(1): 136-138
CrossRef Pubmed Google scholar
[24]
Young M D, Wakefield M J, Smyth G K, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology, 2010, 11(2): R14
CrossRef Pubmed Google scholar
[25]
Mao X, Cai T, Olyarchuk J G, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 2005, 21(19): 3787-3793
CrossRef Pubmed Google scholar
[26]
Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-∆∆CT Method. Methods, 2001, 25(4): 402-408
CrossRef Pubmed Google scholar
[27]
Ling H Q, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Li Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, Zhang B, Wu H, Tang D, Shen Q, Xue P, Zou S, Wang X, Liu X, Wang F, Yang Y, An X, Dong Z, Zhang K, Zhang X, Luo M C, Dvorak J, Tong Y, Wang J, Yang H, Li Z, Wang D, Zhang A, Wang J. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature, 2013, 496(7443): 87-90
CrossRef Pubmed Google scholar
[28]
Luo M C, Gu Y Q, You F M, Deal K R, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen C M, Zhang Y, McGuire P E, Pasternak S, Stein J C, Ware D, Kramer M, McCombie W R, Kianian S F, Martis M M, Mayer K F, Sehgal S K, Li W, Gill B S, Bevan M W, Simková H, Dolezel J, Weining S, Lazo G R, Anderson O D, Dvorak J. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(19): 7940-7945
CrossRef Pubmed Google scholar
[29]
Kawakatsu T, Yamamoto M P, Touno S M, Yasuda H, Takaiwa F. Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. The Plant Journal, 2009, 59(6): 908-920
CrossRef Pubmed Google scholar
[30]
Ravel C, Martre P, Romeuf I, Dardevet M, El-Malki R, Bordes J, Duchateau N, Brunel D, Balfourier F, Charmet G. Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. Plant Physiology, 2009, 151(4): 2133-2144
CrossRef Pubmed Google scholar
[31]
Albani D, Hammond-Kosack M C, Smith C, Conlan S, Colot V, Holdsworth M, Bevan M W. The wheat transcriptional activator SPA: a seed-specific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes. Plant Cell, 1997, 9(2): 171-184
CrossRef Pubmed Google scholar
[32]
Conlan R S, Hammond-Kosack M, Bevan M. Transcription activation mediated by the bZIP factor SPA on the endosperm box is modulated by ESBF-1 in vitro. The Plant Journal, 1999, 19(2): 173-181
CrossRef Pubmed Google scholar
[33]
Guillaumie S, Charmet G, Linossier L, Torney V, Robert N, Ravel C. Colocation between a gene encoding the bZip factor SPA and an eQTL for a high-molecular-weight glutenin subunit in wheat (Triticum aestivum). Genome, 2004, 47(4): 705-713
CrossRef Pubmed Google scholar
[34]
Dong G, Ni Z, Yao Y, Nie X, Sun Q. Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Molecular Biology, 2007, 63(1): 73-84
CrossRef Pubmed Google scholar
[35]
Gibbs B F, Alli I. Characterization of a purified alpha-amylase inhibitor from white kidney bean (Phaseolus vulgaris). Food Research International, 1998, 31(3): 217-225
CrossRef Google scholar
[36]
Feng G H, Richardson M, Chen M S, Kramer K J, Morgan T D, Reeck G R. α-amylase inhibitors from wheat: amino acid sequences and patterns of inhibition of insect and human α-amylases. Insect Biochemistry and Molecular Biology, 1996, 26(5): 419-426
CrossRef Pubmed Google scholar
[37]
Franco O L, Rigden D J, Melo F R, Bloch C Jr, Silva C P, Grossi de Sá M F. Activity of wheat α-amylase inhibitors towards bruchid α-amylases and structural explanation of observed specificities. European Journal of Biochemistry, 2000, 267(8): 2166-2173
CrossRef Pubmed Google scholar
[38]
Lajolo F M, Finardi F F. Partial characterization of the amylase inhibitor of black beans (Phaseolus vulgaris), variety Rico 23. Journal of Agricultural and Food Chemistry, 1985, 33(1): 132-138
CrossRef Google scholar

Acknowledgements

This work was supported by two grants from the National Nature Science Foundation of China (31371607 and 31071412), and a grant from Hi-Tech Research and Development Program of China (2012AA101105).
Supplementary material
The online version of this article at http://dx.doi.org/(doi:10.15302/J-FASE-2014024) contains supplementary material (Appendix A-E).
Compliance with ethics guidelines
Liu Wei, Zhihui Wu, Yufeng Zhang, Dandan Guo, Yuzhou Xu, Weixia Chen, Haiying Zhou, Mingshan You and Baoyun Li declare that they have no conflict of interest or financial conflicts to disclose.
This article does not contain any studies with human or animal subjects performed by any of the authors.

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