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Profiling the differentially expressed genes in two rice varieties during rapid grain-filling stages

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Abstract

Grain filling is an important agronomic trait, which directly affects the final yield of rice. Partially filled and empty rice grains are among the factors that limit the yield of MR219, one of the highest yielding rice varieties in Malaysia. In this study, the NSF 20 K rice oligonucleotide array, which contains 20,000 70-mer oligonucleotide probes, was used for direct comparison of the transcriptomes of MR219 and MR84 (a rice variety that has higher percentage of filled grains compared to MR219), during rapid grain-filling period at 5 and 10 days after fertilization (DAF). A total of 155 and 233 genes were differentially expressed in MR219 compared to MR84 at 5 and 10 DAF, respectively; and 9 of these expression ratios were tested using quantitative real-time RT PCR. Among the differentially expressed genes identified were those encoding hexokinase, various sugar transporters, GSDL-like lipase/acylhydrolase, brassinosteroid-insensitive 1-associated receptor kinase 1 precursor and homeobox protein GLABRA2, which were analyzed by real-time RT PCR in this study. The differences demonstrated by these genes in their transcript levels and profiles, between the two rice varieties understudied at different stages of grain filling may contribute to the formulation of hypotheses toward the understanding of poor percentage of filled grains in MR219.

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Fig. 1
Fig. 2

Abbreviations

aRNA:

Amplified RNA

DAF:

Days after fertilization

DEGs:

Differentially expressed genes

LAE:

Lanatoside 15′-O-acetylesterase

LIMMA:

Linear model for miroarray data

MST:

Monosaccharide transporter

OPT:

Oligopeptide transporter

RT PCR:

Reverse transcription polymerase chain reaction

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang I, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Amaratunga D, Cabrera J (2004) Exploration and analysis of DNA microarray and protein array data. Wiley, Hoboken, p 68

    Google Scholar 

  • Benjamin V, Hochberg V (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57:289–300

    Google Scholar 

  • Cheng WH, Taliercio EW, Chourey PS (1999) Genetic evidence that invertase-mediated release of hexoses is critical for appropriate carbon portioning and normal seed development in maize. Theor Appl Genet 98:485–495

    Article  CAS  Google Scholar 

  • Cheng S, Zhuang J, Fan Y, Du J, Cao L (2007) Progress in research and development on hybrid rice: a super-domesticate in China. Ann Bot 100:959–966

    Article  PubMed  Google Scholar 

  • Cho J-I, Ryoo N, Ko S, Lee S-K, Lee J, Jung K-H, Lee Y-H, Bhoo SH, Winderickx J, An G, Hahn T-R, Jeon J-S (2006) Structure expression and functional analysis of the hexokinase gene family in rice (Oryza sativa L.). Planta 224:598–611

    Article  PubMed  CAS  Google Scholar 

  • Cock JH, Yoshida S (1972) Accumulation of 14C-labelled carbohydrate before flowering and its subsequent redistribution and respiration in the rice plant. Proc Crop Sci Soc Jpn 41:226–264

    Article  CAS  Google Scholar 

  • Dennis DT, Blakeley SD (2000) Chapter 13. Carbohydrate metabolism. In: Buchanan B, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. Am Soc Plant Physiol, Rockville, pp 630–675

    Google Scholar 

  • Gao JW, Liu JZ, Li B, Li ZS (2001) Isolation and purification of functional total RNA from blue grained wheat endosperm tissues containing high levels of starches and flavanoids. Plant Mol Biol Reptr 19:185–185

    Google Scholar 

  • Higgins CF, Payne JW (1981) The peptide pools of germinating barley grains: relation to hydrolysis and transport of storage proteins. Plant Physiol 67:785–792

    Article  PubMed  CAS  Google Scholar 

  • Hirose T, Takano M, Terau T (2002) Cell wall invertase in developing rice caryopsis: molecular cloning of OsCIN1and analysis of its expression in relation to its role in grain filling. Plant Cell Physiol 43:452–459

    Article  PubMed  CAS  Google Scholar 

  • Ho LC (1988) Metabolism and compartmentation of imported sugars in sink organs in relation to sink strength. Annu Rev Plant Physiol Plant Mol Biol 39:355–378

    Article  CAS  Google Scholar 

  • Ishimaru K, Kashiwagi T, Hirotsu N, Madoka Y (2005) Identification and physiological analyses of a locus for rice yield potential across the genetic background. J Exp Bot 56:2745–2753

    Article  PubMed  CAS  Google Scholar 

  • Ito M, Sato Y, Matsuoka M (2002) Involvement of homeobox genes in early body plan of monocot. Int Rev Cytol 218:1–35

    Article  PubMed  CAS  Google Scholar 

  • Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time RT PCR. Biochem Biophys Res Commun 345:646–651

    Article  PubMed  CAS  Google Scholar 

  • Jung K-H, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo Y-S, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia A-P, An K, Chou H-H, Rocke D, Lee GC, Schnable PS, An G, Buell RC, Ronald PC (2009) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS ONE 3:e3337

    Article  Google Scholar 

  • Kandzia R, Grimm R, Eckerskorn C, Lindemann P, Luckner M (1998) Purification and characterization of lanatoside 15-O-acetylesterase from Digitalis lanata Ehrh. Planta 204:383–389

    Article  PubMed  CAS  Google Scholar 

  • Koch KE (1996) Carbohydrate-modulated gene expression in plants. Annu Rev Plant Physiol Plant Mol Biol 47:509–540

    Article  PubMed  CAS  Google Scholar 

  • Koch KE (2004) Sucrose metabolism: regulatory mechanisms and pivotal roles in sugar sensing and plant development. Curr Opin Plant Biol 7:235–246

    Article  PubMed  CAS  Google Scholar 

  • Liang J, Zhang J, Cao X (2001) Grain sink strength may be related to the poor grain filling of indica-japonica rice (Oryza sativa) hybrids. Physiol Plant 112:470–477

    Article  PubMed  CAS  Google Scholar 

  • Lim JD, Cho J-I, Park Y-I, Hann T-R, Choi S-B, Jeon J-S (2006) Sucrose transport from source to sink seeds in rice. Physiol Plant 126:572–584

    Article  CAS  Google Scholar 

  • Miller ME, Chourey PS (1992) The maize invertase-deficient miniature-1 seed mutation is associated with aberrant pedicel and endosperm development. Plant Cell 4:297–305

    Article  PubMed  CAS  Google Scholar 

  • Murchie EH, Yang J, Hubbart S, Horton P, Peng S (2002) Are there associations between grain-filling rate and photosynthesis in the flag leaves of field-grown rice? J Exp Bot 53:2217–2224

    Article  PubMed  CAS  Google Scholar 

  • Peng S, Cassman KG, Virmani SS, Sheehy J, Khush GS (1999) Yield potential trends of tropical since the release of IR8 and its challenge of increasing rice yield potential. Crop Sci 39:1552–1559

    Article  Google Scholar 

  • Peng S, Khush GS, Virk P, Tang Q, Zou Y (2008) Progress in ideotype breeding to increase rice yield potential. Field Crops Res 108:32–38

    Article  Google Scholar 

  • Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article 3

  • Stacey MG, Osawa H, Patel A, Gassmann W, Stacey G (2006) Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta 223:291–305

    Article  PubMed  CAS  Google Scholar 

  • Toyofuku K, Kasahara M, Yamaguchi J (2000) Characterization and expression of monosaccharide transporters (OsMSTs) in rice. Plant Cell Physiol 41:940–947

    Article  PubMed  CAS  Google Scholar 

  • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: research0034.1-0034.11

  • Wang Y, Xu H, Wei X, Chai C, Xiao Y, Zhang Y, Chen B, Xiao G, Ouwerkerk PBF, Wang M, Zhu Z (2007) Molecular cloning and expression analysis of a monosaccharide transporter gene OsMST4 from rice (Oryza sativa L.). Plant Mol Biol 65:439–451

    Article  PubMed  CAS  Google Scholar 

  • Weber H, Borisjuk L, Heim U, Buchner P, Wobus U (1995) Seed coat-associated invertases of faba bean control both unloading and storage functions: cloning of cDNAs and cell-type specific expression. Plant Cell 7:1835–1846

    Article  PubMed  CAS  Google Scholar 

  • Wei G, Tao Y, Liu G, Chen C, Luo R, Xia H, gan Q, Zeng H, Lu Z, Han Y, Li X, Song G, Zhai H, Peng Y, Li D, Xu H, Wei X, Cao M, Deng H, Xin Y, Fu X, Yuan L, Yu J, Zhu Z, Zhu L (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc Natl Acad Sci USA 106:7695–7701

    Article  PubMed  CAS  Google Scholar 

  • Weschke W, Panitz R, Gubatz S, Wang Q, Radchuk R, Weber H, Wobus U (2003) The role of invertases and hexose transporters in controlling sugar ratios in maternal and filial tissues of barley caryopses during early development. Plant J 33:395–411

    Article  PubMed  CAS  Google Scholar 

  • Yamamuro C, Ihara Y, Wu X, Noguchi T, Fujioka S, Takatsuto S, Ashikari M, Kitano H, Matsuoka M (2000) Loss of function of a rice brassinosteroid insensitive 1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 12:1591–1605

    Article  PubMed  CAS  Google Scholar 

  • Yang YH, Paquet AC (2005) Preprocessing two-color spotted arrays. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S (eds) Bioinformatics and computational biology solutions using R and Bioconductor. Springer, New York, p 63

  • Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nature Rev Genet 3:579–588

    PubMed  CAS  Google Scholar 

  • Zhu T, Budworth P, Chen W, Provart N, Chang HS, Guimil S, Su W, Estes B, Zou G, Wang X (2003) Transcriptional control of nutrient partitioning during rice grain filing. J Plant Biotech 1:59–70

    Article  CAS  Google Scholar 

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Acknowledgments

This project was funded by the Intensified Research Grant for Priority Area (IRPA) No. 01-03-03-001BTK/ER/001 from the Ministry of Science, Technology and Innovation (MOSTI) of Malaysia. We wish to thank the Malaysian Agricultural Research and Development Institute for supplying the seeds of MR219 and MR84, Fong-Chin Lee for preparing the RNA template for quantitative real-time RT PCR analyses, and the Malaysia Genome Institute for the microarray scanning service.

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Authors and Affiliations

  1. Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia

    Chin-Jit Teo, Le Vinh Thuc, Wai-Sun Chan, Sudha V. Chivukula, Parameswari Namasivayam & Chai-Ling Ho

  2. Institute of Tropical Agriculture, Universiti Putra Malaysia, Selangor Darul Ehsan, Malaysia

    Keat-Ai Yeoh, Parameswari Namasivayam & Chai-Ling Ho

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  1. Chin-Jit Teo
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  2. Le Vinh Thuc
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  3. Keat-Ai Yeoh
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  5. Sudha V. Chivukula
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  6. Parameswari Namasivayam
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Correspondence to Chai-Ling Ho.

Additional information

Communicated by J.-H. Liu.

Electronic supplementary material

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Supplementary Table 1: DEGs between MR219 and MR84 at 5 DAF and 10 DAF.

Supplementary material 1 (DOC 404 kb)

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Teo, CJ., Vinh Thuc, L., Yeoh, KA. et al. Profiling the differentially expressed genes in two rice varieties during rapid grain-filling stages. Acta Physiol Plant 33, 2259–2268 (2011). https://doi.org/10.1007/s11738-011-0765-1

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  • DOI: https://doi.org/10.1007/s11738-011-0765-1

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