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Map-based cloning of the ERECT PANICLE 3 gene in rice

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Abstract

Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.

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References

  • An S, Park S, Jeong DH, Lee DY, Kang HG, Yu JH, Hur J, Kim SR, Kim YH, Lee M, Han S, Kim SJ, Yang J, Kim E, Wi SJ, Chung HS, Hong JP, Choe V, Lee HK, Choi JH, Nam J, Park PB, Park KY, Kim WT, Choe S, Lee CB, An G (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol 133:2040–2047

    Article  PubMed  CAS  Google Scholar 

  • Cao Y, Yang Y, Zhang H, Li D, Zheng Z, Song F (2008) Overexpression of a rice defense-related F-box protein gene OsDRF1 in tobacco improves disease resistance through potentiation of defense gene expression. Physiol Plant 134:440–452

    Article  PubMed  CAS  Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu KS, Xiao JH, Yu ZH, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    PubMed  CAS  Google Scholar 

  • Chen YL, Zhang QY, Jian YY, Yang YS, Liu KD, Liu YG (2006) A rice panicle mutant created by transformation with an antisense cDNA library. J Integr Plant Biol 48:1300–1305

    Article  CAS  Google Scholar 

  • Chen Y, Wei S, Liu C, Zhou W, Ma Z, Huang D, Liu Y, Chen Q, Yang X, Yang l, Bai D, Li R (2008) Exploitation of molecular markers for erect panicle trait and study on breeding indica erect panicle varieties in rice. Southwest China J Agric Sci 21:6–11

    Google Scholar 

  • Chin J, Kim J, Jiang W, Chu S, Woo M, Han L, Brar D, Koh H (2007) Identification of subspecies-specific STS markers and their association with segregation distortion in rice (Oryza sativa L.). J Crop Sci Biotech 10:175–184

    Google Scholar 

  • Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L, Ehrismann JS, Jurgens G, Estelle M (2005) Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell 9:109–119

    Article  PubMed  CAS  Google Scholar 

  • Donald C (1968) The breeding of crop ideo type. Euphytica 17:385–403

    Article  Google Scholar 

  • Gao S, Chen W, Zhang B (1999) Studies of erect panicle in rice. J Jilin Agric Sci 24:12–15

    Google Scholar 

  • Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, Kitano H, Matsuoka M (2004) GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. Plant J 37:626–634

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez-Carranza ZH, Rompa U, Peters JL, Bhatt AM, Wagstaff C, Stead AD, Roberts JA (2007) Hawaiian skirt: an F-box gene that regulates organ fusion and growth in Arabidopsis. Plant Physiol 144:1370–1382

    Article  PubMed  CAS  Google Scholar 

  • Hepworth SR, Klenz JE, Haughn GW (2006) UFO in the Arabidopsis inflorescence apex is required for floral-meristem identity and bract suppression. Planta 223:769–778

    Article  PubMed  CAS  Google Scholar 

  • Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497

    Article  PubMed  CAS  Google Scholar 

  • Ikeda K, Nagasawa N, Nagato Y (2005) ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice. Dev Biol 282:349–360

    Article  PubMed  CAS  Google Scholar 

  • Ikeda K, Ito M, Nagasawa N, Kyozuka J, Nagato Y (2007) Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate. Plant J 51:1030–1040

    Article  PubMed  CAS  Google Scholar 

  • Itoh H, Matsuoka M, Steber CM (2003) A role for the ubiquitin-26S-proteasome pathway in gibberellin signaling. Trend Plant Sci 8:492–497

    Article  CAS  Google Scholar 

  • Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483

    Article  PubMed  CAS  Google Scholar 

  • Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR (2001) An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410:487–490

    Article  PubMed  CAS  Google Scholar 

  • Ji HS, Chu SH, Jiang W, Cho YI, Hahn JH, Eun MY, McCouch SR, Koh HJ (2006) Characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes. Genetics 173:995–1005

    Article  PubMed  CAS  Google Scholar 

  • Kipreos ET, Pagano M (2000) The F-box protein family. Genome Biol 1:Reviews 3002

    Google Scholar 

  • Kong FN, Wang JY, Zou JC, Shi LX, Jin DM, Xu ZJ, Wang B (2007) Molecular tagging and mapping of the erect panicle gene in rice. Mol Breed 19:297–304

    Article  CAS  Google Scholar 

  • Kosambi D (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Lin SY, Ikehashi H, Yanagihara S, Kawashima A (1992) Segregation distortion via male gametes in hybrids between indica and japonica or wide-compatibility varieties of rice (Oryza Sativa L). Theor Appl Genet 84:812–818

    Article  Google Scholar 

  • Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Liu YG (2008) Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc Natl Acad Sci USA 105:18871–18876

    Article  PubMed  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    Article  PubMed  CAS  Google Scholar 

  • Ni W, Xie D, Hobbie L, Feng B, Zhao D, Akkara J, Ma H (2004) Regulation of flower development in Arabidopsis by SCF complexes. Plant Physiol 134:1574–1585

    Article  PubMed  CAS  Google Scholar 

  • Otsuka K, Kalirajan KP (2006) Rice green revolution in Asia and its transferability to Africa: an introduction. Dev Econ 44:107–122

    Google Scholar 

  • Qiao Y, Jiang W, Rahman ML, Chu SH, Piao R, Han L, Koh HJ (2008) Comparison of molecular linkage maps and QTLs for morphological traits in two reciprocal backcross populations of rice. Mol Cells 25:417–427

    PubMed  CAS  Google Scholar 

  • Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963

    Article  CAS  Google Scholar 

  • Scarpella E, Rueb S, Meijer AH (2003) The RADICLELESS1 gene is required for vascular pattern formation in rice. Development 130:645–658

    Article  PubMed  CAS  Google Scholar 

  • Schultz TF, Kiyosue T, Yanovsky M, Wada M, Kay SA (2001) A role for LKP2 in the circadian clock of Arabidopsis. Plant Cell 13:2659–2670

    Article  PubMed  CAS  Google Scholar 

  • Shimizu M, Takeoka Y (1965) Effects of gibberellin on the development of vascular bundles in panicles. Jpn J Crop Sci 35:105–112

    Google Scholar 

  • Yan CJ, Zhou XH, Yan S, Chen F, Yeboah M, Tang SZ, Liang GH, Gu MH (2007) Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theor Appl Genet 115:1093–1100

    Article  PubMed  CAS  Google Scholar 

  • Yin H (1961) The research about rice and wheat population. Shanghai Scientific and Technical Publisher, Shanghai, pp 44–50

    Google Scholar 

  • Zhang WZ, Xu ZJ, Zhang LB, Chen WF, Qiu FL, Shao GJ, Hua ZT (2002) Analysis on evolution for the erect panicle type varieties of rice. J Shenyang Agric Univ 33:161–166

    Google Scholar 

  • Zhou J, Xu Y, Xu P, Deng X, Hu F, Li J, Ren G, Tao D (2008) Introgression and mapping of erect panicle gene from Oryza glaberrma in to Oryza Sativa. Rice Genet Newsl 24:18–21

    CAS  Google Scholar 

  • Zhu LH, Gu MH (1979) The inheritance of rice grain shattering. Hereditas 1:17–19

    Google Scholar 

Download references

Acknowledgments

This research was supported by a grant (code#CG3111) from the Crop Functional Genomics Center of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology, Republic of Korea.

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Authors and Affiliations

  1. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Rihua Piao, Wenzhu Jiang, Tae-Ho Ham, Min-Seon Choi, Yongli Qiao, Sang-Ho Chu, Jung-Hyun Park, Mi-Ok Woo, Joohyun Lee & Hee-Jong Koh

  2. Agricultural College, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China

    Zhengxun Jin

  3. National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea

    Gynheung An

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  1. Rihua Piao
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  2. Wenzhu Jiang
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  3. Tae-Ho Ham
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  4. Min-Seon Choi
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  5. Yongli Qiao
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  9. Zhengxun Jin
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  10. Gynheung An
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  11. Joohyun Lee
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  12. Hee-Jong Koh
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Correspondence to Hee-Jong Koh.

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Communicated by T. Tai.

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Piao, R., Jiang, W., Ham, TH. et al. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet 119, 1497–1506 (2009). https://doi.org/10.1007/s00122-009-1151-x

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  • DOI: https://doi.org/10.1007/s00122-009-1151-x

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