Skip to main content
SpringerLink
Log in

Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

In rice, at the stage from pistil and stamen primordia formation to microsporocyte meiosis, the young panicle organs (YPO) make a great contribution to grain productivity. This period corresponds to the onset of meiosis and marks the transition from vegetative to reproductive stages. By comparing gene expression profiling of YPO with that of rice aerial vegetative organs (AVO), it is possible to gain further molecular insight into this period that is developmentally and functionally important. In this report, a total of 92,582 high-quality ESTs from 5′-end sequencing, including 44,247 from YPO and 48,335 from AVO, were obtained and classified. There were 12,884 (29.12%) ESTs from YPO and 16,304 (33.73%) ESTs from AVO matched to known genes, which generated 1,667 and 2,172 known genes, respectively, after integration of these ESTs. From the functions of known homologous genes, we identified some tissue- and developmental-stage-specified genes in YPO. The expression of these genes clearly reflected the unique functional characteristics of YPO. Furthermore, we estimated that there are about 10,000 mRNAs specifically expressed in rice YPO.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Alvarez-Buylla ER, Pelaz S, Liljegren SJ, Gold SE, Burgeff C, Ditta GS, Ribas de Pouplana L, Martinez-Castilla L, Yanofsky MF (2000) An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci USA 97:5328–5333

    Article  PubMed  CAS  Google Scholar 

  • Banerjee A (2002) Coordination of posttranslational modifications of bovine brain alpha-tubulin. Polyglycylation of delta2 tubulin. J Biol Chem 277:46140–46144

    Article  PubMed  CAS  Google Scholar 

  • Burgeff C, Liljegren SJ, Tapia-Lopez R, Yanofsky MF, Alvarez-Buylla ER (2002) MADS-box gene expression in lateral primordia, meristems and differentiated tissues of Arabidopsis thaliana roots. Planta 214:365–372

    Article  PubMed  CAS  Google Scholar 

  • Busi MV, Bustamante C, D’Angelo C, Hidalgo-Cuevas M, Boggio SB, Valle EM, Zabaleta E (2003) MADS-box genes expressed during tomato seed and fruit development. Plant Mol Biol 52:801–815

    Article  PubMed  CAS  Google Scholar 

  • Cao Y, Fu B, Wang M (1987) Initial analysis of protein using 2-D gel in photoperiod-sensitive genic male sterile line in rice (Oryza sativa L.). J Wuhan Univ (HPGMR Specific Issue) 1:73–80

    Google Scholar 

  • Cao M, Zheng Y, Zhang Q (1992) Comparative analysis of protein using 2-D gel between photoperiod-sensitive genic male sterile line Nongken 58S and fertile line 58N in rice (Oryza sativa L.). J Huazhong Agric Univ 11:305–311

    Google Scholar 

  • Carpenter JL, Ploense SE, Snustad DP, Silflow CD (1992) Preferential expression of an alpha-tubulin gene of Arabidopsis in pollen. Plant Cell 4:557–571

    Article  PubMed  CAS  Google Scholar 

  • Caryl AP, Armstrong SJ, Jones GH, Franklin FC (2000) A homologue of the yeast HOP1 gene is inactivated in the Arabidopsis meiotic mutant asy1. Chromosoma 109:62–71

    Article  PubMed  CAS  Google Scholar 

  • Chen Q, Atkinson A, Otsuga D, Christensen T, Reynolds L, Drews GN (1999) The Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation. Development 126:2715–2726

    PubMed  CAS  Google Scholar 

  • Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9:950–959

    Article  PubMed  CAS  Google Scholar 

  • Fagard M, Boutet S, Morel JB, Bellini C, Vaucheret H (2000) AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc Natl Acad Sci USA 97:11650–11654

    Article  PubMed  CAS  Google Scholar 

  • Feng J, Lu Y, Liu X (2000) Cytological mechanism of pollen abortion in photoperiod-temperature sensitive genic male sterile line Peiai 64S in rice (Oryza sativa L.). Chin J Rice Sci 14:7–14

    Google Scholar 

  • Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320

    Article  PubMed  CAS  Google Scholar 

  • Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V (2002) Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol 128:896–910

    Article  PubMed  Google Scholar 

  • Francisco VS, Leon MC, Elena RAB (2000) MADS-box genes: development and evolution of plant body plans. J Phycol 36:803–812

    Article  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    Article  PubMed  CAS  Google Scholar 

  • Hanfrey C, Franceschetti M, Mayer MJ, Illingworth C, Michael AJ (2002) Abrogation of upstream open reading frame-mediated translational control of a plant S-adenosylmethionine decarboxylase results in polyamine disruption and growth perturbations. J Biol Chem 277:44131–44139

    Article  PubMed  CAS  Google Scholar 

  • Jack T (2001) Plant development going MADS. Plant Mol Biol 46:515–520

    Article  PubMed  CAS  Google Scholar 

  • Jang S, An K, Lee S, An G (2002) Characterization of tobacco MADS-box genes involved in floral initiation. Plant Cell Physiol 43:230–238

    Article  PubMed  CAS  Google Scholar 

  • Jansen MAK, Sessa G, Malkin S, Fluhr R (1992) PEPC-mediated carbon fixation in transmitting tract cells reflects style-pollen tube interactions. Plant J 2:507–515

    Article  CAS  Google Scholar 

  • Jin H, Martin C (1999) Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol 41:577–585

    Article  PubMed  CAS  Google Scholar 

  • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379

    Article  PubMed  Google Scholar 

  • Lan L, Chen W, Lai Y, Suo J, Kong Z, Li C, Lu Y, Zhang Y, Zhao X, Zhang X, Han B, Cheng J, Xue Y (2004) Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice (Oryza sativa L.) with a 10K cDNA microarray. Plant Mol Biol 54:471–487

    Article  PubMed  CAS  Google Scholar 

  • Liu G, Grant WM, Persky D, Latham VM Jr, Singer RH, Condeelis J (2002) Interactions of elongation factor 1alpha with F-actin and beta-actin mRNA: implications for anchoring mRNA in cell protrusions. Mol Biol Cell 13:579–592

    Article  PubMed  CAS  Google Scholar 

  • Mad Arif SA, Taylor MA, George LA, Butler AR, Burch LR, Davies HV, Stark MJ, Kumar A (1994) Characterisation of the S-adenosylmethionine decarboxylase (SAMDC) gene of potato. Plant Mol Biol 26:327–338

    Article  PubMed  CAS  Google Scholar 

  • Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9:1143–1155

    Article  PubMed  CAS  Google Scholar 

  • Moore G (1995) Cereal genome evolution: pastoral pursuits with ‘Lego’ genomes. Curr Opin Genet Dev 5:717–724

    Article  PubMed  CAS  Google Scholar 

  • Prasad K, Sriram P, Kumar CS, Kushalappa K, Vijayraghavan U (2001) Ectopic expression of rice OsMADS1 reveals a role in specifying the lemma and palea, grass floral organs analogous to sepals. Dev Genes Evol 211:281–290

    Article  PubMed  CAS  Google Scholar 

  • Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569

    Article  Google Scholar 

  • Rogers HJ, Greenland AJ, Hussey PJ (1993) Four members of the maize beta-tubulin gene family are expressed in the male gametophyte. Plant J 4:875–882

    Article  PubMed  CAS  Google Scholar 

  • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329

    Article  PubMed  CAS  Google Scholar 

  • Saedler H, Becker A, Winter KU, Kirchner C, Theissen G (2001) MADS-box genes are involved in floral development and evolution. Acta Biochim Pol 48:351–358

    PubMed  CAS  Google Scholar 

  • Sakaki Y, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141

    Article  Google Scholar 

  • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316

    Article  PubMed  CAS  Google Scholar 

  • Sawa S, Watanabe K, Goto K, Liu YG, Shibata D, Kanaya E, Morita EH, Okada K (1999) FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev 13:1079–1088

    PubMed  CAS  Google Scholar 

  • Shen B, Li C, Tarczynski MC (2002) High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene. Plant J 29:371–380

    Article  PubMed  CAS  Google Scholar 

  • Siegfried KR, Eshed Y, Baum SF, Otsuga D, Drews GN, Bowman JL (1999) Members of the YABBYgene family specify abaxial cell fate in Arabidopsis. Development 126:4117–4128

    PubMed  CAS  Google Scholar 

  • Sung SS, Sheihw J, Geigerd R, Black C (1994) Growth, sucrose synthase, and invertase activities of developing Phaseolus vulgaris L. fruits. Plant Cell Environ 17:419–426

    Article  CAS  Google Scholar 

  • Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543

    Article  PubMed  CAS  Google Scholar 

  • Weig A, Deswarte C, Chrispeels MJ (1997) The major intrinsic protein family of Arabidopsis has 23 members that form three distinct groups with functional aquaporins in each group. Plant Physiol 114:1347–1357

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Tang JB, Walker MG, Zhang XQ, Wang J, Hu SN, Xu HY, Deng YJ, Dong JH, Ye L, Li L, Li J, Wang XG, Xu H, Pan YB, Lin W, Tian W, Liu J, Wei LP, Li SQ, Yang HM, Yu J, Wang J (2003) Gene identification and expression analysis of 86,136 expressed sequence tags (EST) from the rice genome. Geno Prot Bioinfo 1:26–42

    CAS  Google Scholar 

Download references

Acknowledgements

The authors are grateful to all the members in Beijing Genomics Institute, who have done EST sequencing and kindly provided the facility for sequence analysis. We thank Jim Henle for his help in improving the readability of this manuscript. This work was supported by project grants from the Chinese Academy of Sciences to J.Y. and H.Y. and by the grants to L.H.Zh. from the National Natural Science Foundation of China (90208001), China High Technology Research and Development Program (2004AA2111310) and Chinese Academy of Sciences (KSCX2-SW-306).

Author information

Authors and Affiliations

  1. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Jiabin Tang, Hong’ai Xia, Dayong Li, Yong Tao & Lihuang Zhu

  2. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, 101300, China

    Jiabin Tang, Hong’ai Xia, Wei Tong, Xiuqing Zhang, Songnian Hu, Jian Wang, Jun Yu, Huanming Yang & Lihuang Zhu

  3. National Hybrid Rice R & D Center, Changsha, 410125, China

    Cao Mengliang

Authors
  1. Jiabin Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hong’ai Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dayong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cao Mengliang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yong Tao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiuqing Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Songnian Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jun Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Huanming Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Lihuang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lihuang Zhu.

Additional information

Jiabin Tang and Hong’ai Xia contributed equally to this work

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tang, J., Xia, H., Li, D. et al. Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions. Mol Genet Genomics 274, 467–476 (2005). https://doi.org/10.1007/s00438-005-0043-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-005-0043-2

Keywords

Search

Navigation