Fine Mapping and Cloning of Leafy Head Mutant Gene pla1-5 in Rice

doi:10.1016/S1672-6308(13)60140-7

Abstract

Abstract:

We identified a leafy head mutant pla1-5 (plastochron 1-5) from the progeny of japonica rice cultivar Taipei 309 treated with 60Co-γ ray irradiation. The pla1-5 mutant has a dwarf phenotype and small leaves. Compared with its wild type, pla1-5 has more leaves and fewer tillers, and it fails to produce normal panicles at the maturity stage. Genetic analysis showed that the pla1-5 phenotype is controlled by a single recessive nuclear gene. Using the map-based cloning strategy, we narrowed down the location of the target gene to a 58-kb region between simple sequence repeat markers CHR1027 and CHR1030 on the long arm of chromosome 10. The target gene cosegregated with molecular markers CHR1028 and CHR1029. There were five predicted genes in the mapped region. The results from sequencing analysis revealed that there was one base deletion in the first exon of LOC_Os10g26340 encoding cytochrome P450 CYP78A11 in the pla1-5 mutant, which might result in a downstream frame shift and premature termination. These results suggest that the P450 CYP78A11 gene is the candidate gene of PLA1-5.

Key words: Oryza sativa, leafy head mutant, genetic analysis, gene cloning, P450 CYP78A11 gene

FENG Gong-Neng, ZHANG Chang-Quan, ZHAO Dong-Sheng, ZHU Kong-Zhi, TU Huai-Zhou, XU Chen-Wu, LIU Qiao-Quan. Fine Mapping and Cloning of Leafy Head Mutant Gene pla1-5 in Rice[J]. RICE SCIENCE, 2013, 20(5): 329-335.

References

Bowman J L, Alvarez J, Weigel D, Meyerowitz E M, Smyth D R. 1993. Control of flower development in Arabidopsis thaliana by APETA1 and interacting genes. Development, 119(3): 721–743.
Chaudhury A M, Letham S, Craig S, Dennis E S. 1993. amp1: A mutant with high cytokinin levels and altered embryonic pattern, faster vegetative growth, constitutive photomorphogenesis and precocious flowering. Plant J, 4(6): 907–916.
Chu H W, Qian Q, Liang W Q, Yin C S, Tan H X, Yao X, Yuan Z, Yang J, Huang H, Luo D, Ma H, Zhang D B. 2006. The FLORAL ORGAN NUMBER4 gene encoding a putative ortholog of Arabidopsis CLAVATA3 regulates apical meristem size in rice. Plant Physiol, 142(3): 1039–1052.
Dellaporta S L, Wood J, Hicks J B. 1983. A plant DNA minipreparation: Version II. Plant Mol Biol Rep, 1(4): 19–21.
Duan Y L, Li W M, Wu W R, Pan R S, Zhou Y C, Qi J M, Ling L H, Chen Z W, Mao D M, Liu H Q, Zhang D F, Xue Y B. 2003a. Genetic analysis and molecular marker mapping of rice panicle differentiation regulating gene fzp(t). Sci China: Ser C, 33(1): 27–32. (in Chinese)
Duan Y L, Wu W R, Liu H Q, Zhang D F, Zhou Y C, Pan R S, Lin L H, Chen Z W, Guan H Z, Mao D M, Li W M, Xue Y B. 2003b. Genetic analysis and gene mapping of leafy head (lhd), a mutant blocking the differentiation of rachis branches in rice (Oryza sativa L.). Chin Sci Bull, 48(20): 2201–2205.
Evans M M S, Poethig R S. 1997. The viviparous8 mutation delays vegetative phase change and accelerates the rate of seedling growth in maize. Plant J, 12(4): 769–779.
Gao Z S, Sugita S, Ikeda S, Cai H W, Sasaki T, Liang G H. 2002. Linkage of AFLP markers to lhd 1, a recessive heterochronic gene in Italian ryegrass. Genome, 45(4): 752–758.
Guan H Z, Duan Y L, Liu H Q, Chen Z W, Zhuo M, Zhuang L J, Qi W M, Pan R S, Mao D M, Zhou Y C, Wang F, Wu W R. 2011. Genetic analysis and fine mapping of an enclosed panicle mutant esp2 in rice (Oryza sativa L.). Chin Sci Bull, 56(14): 1476–1480.
Hu C H. 1961. An X-ray induced panicle-degenerating mutant in rice. Jpn J Breeding, 11(1): 19–23. (in Japanese with English summary)
Irish V F. 2010. The flowering of Arabidopsis flower development. Plant J, 61(6): 1014–1028.
Itoh J I, Hasegawa A, Kitano H, Nagato Y. 1998. A recessive heterochronic mutation, plastochron 1, shortens the plastochron and elongates the vegetative phase in rice. Plant Cell, 10(9): 1511–1521.
Jiang L, Qian Q, Mao L, Zhou Q Y, Zhai W X. 2005. Characterization of the rice floral organ number mutant fon3. J Integr Plant Biol, 47(1): 100–106.
Kawakatsu T, Itoh J I, Miyoshi K, Kurata N, Alvarez N, Veit B, Nagato Y. 2006. PLASTOCHRON 2 regulates leaf initiation and maturation in rice. Plant Cell, 18(3): 612–625.
Kawakatsu T, Taramino G, Itoh J I, Allen J, Sato Y, Hong S K, Yule R, Nagasawa N, Kojima M, Kusaba M, Sakakibara H, Sakai H, Nagato Y. 2009. PLASTOCHRON3/GOLIATH encodes a glutamate carboxypeptidase required for proper development in rice. Plant J, 58(6): 1028–1040.
Kaufmann K, Mui?o J M, Jauregui R, Airoldi C A, Smaczniak C, Krajewski P, Angenent G C. 2009. Target genes of the MADS transcription factor SEPALLATA3: Integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol, 7: e1000090.
Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J. 2003. FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development, 130(16): 3841–3850.
Li S B, Qian Q, Fu Z M, Zeng D L, Meng X B, Kyozuka J, Maekawa M, Zhu X D, Zhang J, Li J Y, Wang Y H. 2009. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. Plant J, 58(4): 592–605.
Michelmore R W, Paran I, Kesseli R V. 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(21): 9828–9832.
Mimura M, Nagato Y, Itoh J I. 2012. Rice PLASTOCHRON genes regulate leaf maturation downstream of the gibberellin signal transduction pathway. Planta, 235(5): 1081–1089.
Miyoshi K, Ahn B O, Kawakatsu T, Ito Y, Itoh J I, Nagato Y, Kurata N. 2004. PLASTOCHRON 1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. Proc Natl Acad Sci USA, 101(3): 875–880.
Moon S, Jung K H, Lee D E, Lee D Y, Lee J, An K, Kang H G, An G. 2006. The rice FON1 gene controls vegetative and reproductive development by regulating shoot apical meristem size. Mol Cells, 21(1): 147–152.
Schuler M A. 1996. Plant cytochrome P450 monooxygenases. Crit Rev Plant Sci, 15(3): 235–284.
Suzaki T, Toriba T, Fujimoto M, Tsutsumi N, Kitano H, Hirano H Y. 2006. Conservation and diversification of meristem maintenance mechanism in Oryza sativa: Function of the FLORAL ORGAN NUMBER2 gene. Plant Cell Physiol, 47(12): 1591–1602.
Wu L W, Jiang H, Hu J, Hu X M, Gao Z Y, Zeng D L, Zhu G L, Dong G J, Qian Q, Guo L B. 2009. Genetic analysis and fine- mapping of a Leafy Head 3 mutant in rice. Chin J Rice Sci, 23(6): 583–588. (in Chinese with English abstract)
Xiong G S, Hu X M, Jiao Y Q, Yu Y C, Chu C C, Li J Y, Qian Q, Wang Y H. 2006. LEAFY HEAD 2, which encodes a putative RNA-binding protein, regulates shoot development of rice. Cell Res, 16(3): 267–276.
Yant L, Mathieu J, Dinh T T, Ott F, Lanz C, Wollmann H, Chen X M, Schmid M. 2010. Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell, 22(7): 2156–2170.
Zhu Q H, Hoque M S, Dennis E S, Upadhyaya N M. 2003. Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L). BMC Plant Biol, 3(1): 6.
Zhu Q H, Dennis E S, Upadhyaya N M. 2007. compact shoot and leafy head 1, a mutation affects leaf initiation and developmental transition in rice (Oryza sativa L.). Plant Cell Rep, 26(4): 421– 427.

[1]	XIA Xiaodong, ZHANG Xiaobo, WANG Zhonghao, CHENG Benyi, Sun Huifeng, XU Xia, GONG Junyi, YANG Shihua, WU Jianli, SHI Yongfeng, XU Rugen. Mapping and Functional Analysis of LE Gene in a Lethal Etiolated Rice Mutant at Seedling Stage [J]. Rice Science, 2023, 30(6): 13-.
[2]	Md. Dhin Islam, Adam H. Price, Paul D. Hallett. Effects of Root Growth of Deep and Shallow Rooting Rice Cultivars in Compacted Paddy Soils on Subsequent Rice Growth [J]. Rice Science, 2023, 30(5): 459-472.
[3]	Sheikh Faruk Ahmed, Hayat Ullah, May Zun Aung, Rujira Tisarum, Suriyan Cha-Um, Avishek Datta. Iron Toxicity Tolerance of Rice Genotypes in Relation to Growth, Yield and Physiochemical Characters [J]. Rice Science, 2023, 30(4): 321-334.
[4]	Yousef Alhaj Hamoud, Hiba Shaghaleh, Wang Ruke, Willy Franz Gouertoumbo, Amar Ali Adam hamad, Mohamed Salah Sheteiwy, Wang Zhenchang, Guo Xiangping. Wheat Straw Burial Improves Physiological Traits, Yield and Grain Quality of Rice by Regulating Antioxidant System and Nitrogen Assimilation Enzymes under Alternate Wetting and Drying Irrigation [J]. Rice Science, 2022, 29(5): 473-488.
[5]	Nie Yuanyuan, Xia Hui, Ma Xiaosong, Lou Qiaojun, Liu Yi, Zhang Anling, Cheng Liang, Yan Longan, Luo Lijun. Dissecting Genetic Basis of Deep Rooting in Dongxiang Wild Rice [J]. Rice Science, 2022, 29(3): 277-287.
[6]	Chen Wei, Cai Yicong, Shakeel Ahmad, Wang Yakun, An Ruihu, Tang Shengjia, Guo Naihui, Wei Xiangjin, Tang Shaoqing, Shao Gaoneng, Jiao Guiai, Xie Lihong, Hu Shikai, Sheng Zhonghua, Hu Peisong. NRL3 Interacts with OsK4 to Regulate Heading Date in Rice [J]. Rice Science, 2022, 29(3): 237-246.
[7]	Shuting Yuan, Chunjue Xu, Wei Yan, Zhenyi Chang, Xingwang Deng, Zhufeng Chen, Jianxin Wu, Xiaoyan Tang. Alternative Splicing of OsRAD1 Defines C-Terminal Domain Essential for Protein Function in Meiosis [J]. Rice Science, 2020, 27(4): 289-301.
[8]	Vijayaraghavareddy Preethi, Xinyou Yin, C. Struik Paul, Makarla Udayakumar, Sreeman Sheshshayee. Responses of Lowland, Upland and Aerobic Rice Genotypes to Water Limitation During Different Phases [J]. Rice Science, 2020, 27(4): 345-354.
[9]	Hussain Kashif, Yingxing Zhang, Anley Workie, Riaz Aamir, Abbas Adil, Hasanuzzaman Rani Md., Hong Wang, Xihong Shen, Liyong Cao, Shihua Cheng. Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza rufipogon [J]. Rice Science, 2020, 27(3): 246-254.
[10]	Radhesh Krishnan Subramanian, Muthuramalingam Pandiyan, Pandian Subramani, Banupriya Ramachandradoss, Chithra Gunasekar, Ramesh Manikandan. Sprouted Sorghum Extract Elicits Coleoptile Emergence, Enhances Shoot and Root Acclimatization, and Maintains Genetic Fidelity in indica Rice [J]. Rice Science, 2018, 25(2): 61-72.
[11]	Nurdiani Dini, Widyajayantie Dwi, Nugroho Satya. OsSCE1 Encoding SUMO E2-Conjugating Enzyme Involves in Drought Stress Response of Oryza sativa [J]. Rice Science, 2018, 25(2): 73-81.
[12]	Fernando Polesi Luís, Bruder Silveira Sarmento Silene, Guidolin Canniatti-Brazaca Solange. Starch Digestibility and Functional Properties of Rice Starch Subjected to Gamma Radiation [J]. Rice Science, 2018, 25(1): 42-51.
[13]	Singh Bhupinder, Raja Reddy Kambham, Diaz Redoña Edilberto, Walker Timothy. Screening of Rice Cultivars for Morpho-Physiological Responses to Early-Season Soil Moisture Stress [J]. Rice Science, 2017, 24(6): 322-335.
[14]	Jini D., Joseph B.. Physiological Mechanism of Salicylic Acid for Alleviation of Salt Stress in Rice [J]. Rice Science, 2017, 24(2): 97-108.
[15]	Fernando Polesi Luís, Divino da Matta Junior Manoel, Bruder Silveira Sarmento Silene, Guidolin Canniatti-Brazaca Solange. Starch Digestibility and Physicochemical and Cooking Properties of Irradiated Rice Grains [J]. Rice Science, 2017, 24(1): 48-55.