Phenotypic analysis of a dwarf and deformed flower3 (ddf3) mutant in rice (Oryzasativa L.) and characterization of candidate genes
WANG Yu-peng, TANG shuang-qin, WU Zhi-feng, SHI Qing-hua, WU Zi-ming
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/Collaborative Innovation Center for the Modernization Production of Double Cropping Rice/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, P.R.China
Abstract Dwarf mutants are the crucial resources for molecular biology research and rice breeding. Here, a rice mutant, dwarf and deformed flower3 (ddf3), was identified in tissue culture of Oryza sativacv. Dongjin. Compared with wild type, the ddf3mutant exhibited severe dwarfism, a greater number of tillers and significantly decreased fertility. In addition, leaf length, panicle length, and grain length, were significantly shorter. All internodes of ddf3were shorter than those of wild type, and histological analysis revealed that internode cell elongation was significantly inhibited in ddf3. In the ddf3mutant, pollen activity was significantly decreased, and the development of most stigmas was abnormal. Genetic analysis indicated that the ddf3mutant phenotypes are controlled by a single or tightly linked nuclear genes. Using an F2 mapping population generated from a cross between ddf3and Yangdao 6 (9311), the DDF3 gene was mapped to a 45.21-kb region between insertion-deletion (InDel) markers M15 and M16 on the long arm of chromosome 7. Sequencing revealed a 13.98-kb-deletion in this region in the ddf3 mutant genome that resulted in the complete or partial deletion of ZF (DHHC type zinc finger protein), EP (expressed protein), and FH2 (actin-binding FH2 domain-containing protein) genes. Quantitative RT-PCR analyses revealed that in wild type, the transcript levels of FH2 were almost the same in all organs, while ZF was mainly expressed in the panicle, and no expression of EP was detected in any organ. Based on these results, ZF and FH2 could be potential DDF3 candidate genes involved in the regulation of rice morphology and flower organ development. Our work has laid the foundation for future functional analysis of these candidate genes and has provided a profitable gene resource for rice breeding for increased fertility in the future.
The research was supported by the National Natural Science Foundation of China (31560350 and 31760350) and the Science and Technology Program of Jiangxi, China (20171ACF60018).
WANG Yu-peng, TANG shuang-qin, WU Zhi-feng, SHI Qing-hua, WU Zi-ming.
2018.
Phenotypic analysis of a dwarf and deformed flower3 (ddf3) mutant in rice (Oryzasativa L.) and characterization of candidate genes. Journal of Integrative Agriculture, 17(05): 1057-1065.
Banerjee J, Maiti M K. 2010. Functional role of rice germin-like protein1 in regulation of plant height and disease resistance. Biochemical and Biophysical Research Communications, 394, 178–183.
Chae K, Kieslich C A, Morikis D, Kim S C, Lord E M. 2009. A gain-of-function mutation of Arabidopsis lipid transfer protein 5 disturbs pollen tube tip growth and fertilization. The Plant Cell, 21, 3902–3914.
Cheung A Y, Niroomand S, Zou Y J, Wu H M. 2010. A transmembrane formin nucleates subapical actin assembly and controls tip-focused growth in pollen tubes. Proceedings of the National Academy of Sciences of the United States of America, 107, 16390–16395.
Daviere J M, Achard P. 2013. Gibberellin signaling in plants. Development, 140, 1147–1151.
Deng Z Y, Liu L T, Li T, Yan S, Kuang B J, Huang S J, Yan C J, Wang T. 2014. OsKinesin-13A is an active microtubule depolymerase involved in glume length regulation via affecting cell elongation. Scientific Reports, 5, 1702–1710.
Ding Z, Lin Z, Li Q, Wu H, Xiang C, Wang J. 2015. DNL1, encodes cellulose synthase-like D4, is a major QTL for plant height and leaf width in rice (Oryza sativa L.). Biochemical and Biophysical Research Communications, 457, 133–140.
Duan Y L, Guan H Z, Ming Z, Chen Z W, Li W T, Pan R S, Mao D M, Zhou Y C, Wu W R. 2012a. Genetic analysis and mapping of an enclosed panicle mutant locus esp1 in rice (Oryza sativa L.). Journal of Integrative Agriculture, 11, 1933–1939.
Duan Y L, Li S P, Chen Z W, Zheng L L, Diao Z J, Zhou Y C, Lan T, Guan H Z, Pan R S, Xue Y B, Wu W R. 2012b. Dwarf and deformed flower 1, encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativa L.). The Plant Journal, 72, 829–842.
Hemsley P A, Kemp A C, Grierson C S. 2005. The TIP GROWTH DEFECTIVE1 S-acyl transferase regulates plant cell growth in Arabidopsis. The Plant Cell, 17, 2554–2563.
Jiang S Y, Cai M, Ramachandran S. 2007. ORYZA SATIVA MYOSIN XI B controls pollen development by photoperiod-sensitive protein localizations. Developmental Biology, 304, 579–592.
Krag E, Nielsen P B. 1989. Analysis on difference of dry matter production between rice cultivars with different plant height in relation to gas diffusion inside stands. Japanese Journal of Crop Science, 58, 374–382.
Li G, Liang W, Zhang X, Ren H, Hu J, Bennett M J, Zhang D. 2014. Rice actin-binding protein RMD is a key link in the auxin-actin regulatory loop that controls cell growth. Proceedings of the National Academy of Sciences of the United States of America, 111, 10377–10382.
Li Y, Lin J, Li L, Peng Y, Wang W, Zhou Y, Tang D, Zhao X, Yu F, Liu X. 2016. DHHC-cysteine-rich domain S-acyltransferase protein family in rice: Organization, phylogenetic relationship and expression pattern during development and stress. Plant Systematics and Evolution, 302, 1405–1417.
Li Z B. 1980. A preliminary discussion about the classification of male sterile lines of rice in China. Acta Agronomica Sinica, 6, 27–34. (in Chinese)
Murray M G, Thompson W F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4325.
Qi B, Doughty J, Hooley R. 2013. A golgi and tonoplast localized S-acyl transferase is involved in cell expansion, cell division, vascular patterning and fertility in Arabidopsis. New Phytologist, 200, 444–456.
Sato Y, Sentoku N, Miura Y, Hirochika H, Kitano H, Matsuoka M. 1999. Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. The EMBO Journal, 18, 992–1002.
Screpanti C, Fonne-Pfister R, Lumbroso A, Rendine S, Lachia M, De Mesmaeker A. 2016. Strigolactone derivatives for potential crop enhancement applications. Bioorganic & Medicinal Chemistry Letters, 26, 2392–2400.
Song L K, Lee S, Kim H J, Hong G N, An G. 2008. OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a. Plant Physiology, 145, 1484–1494.
Wang J X, Jian S, Li C X, Liu H L, Wang J G, Zhao H W, Zou D T. 2016. Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions. Journal of Integrative Agriculture, 15, 2688–2702.
Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J. 2010. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiology, 153, 1747–1758.
Xiang X C, Zhang X H, Xu Y F, Long X L, Zhang Y L. 2011.Identification of a new sterile cytoplasmic fertility line H236A from indica Miyang 46. Journal of Plant Genetic Resources, 12, 1014–1018.
Yang W, Ren S, Zhang X, Gao M, Ye S, Qi Y, Zheng Y, Wang J, Zeng L, Li Q. 2011. BENT UPPERMOST INTERNODE1 encodes the class II formin FH5 crucial for actin organization and rice development. The Plant Cell, 23, 661–680.
Ye H, Li L, Yin Y. 2011. Recent advances in the regulation of brassinosteroid signaling and biosynthesis pathways. Journal of Integrative Plant Biology, 53, 455–468.
Yu S, Liu H, Luo L. 2007. Analysis of relative gene expression using different real-time quantitative PCR. Acta Agronomica Sinica, 33, 1214–1218. (in Chinese)
Zhang L, Guo S, Wang L, Zhang T Q, Zhuang H. 2015. Gene mapping and candidate gene analysis of a dwarf and deformed flower 2 (ddf2) mutant in rice (Oryza sativa). Scientia Agricultura Sinica, 48, 1873–1881. (in Chinese)
Zhang Q, Shen B Z, Dai X K, Mei M H, Maroof M A S, Li Z B. 1994. Using bulked extremes and recessive class to map genes for photoperiod-sensitive genic male sterility in rice. Proceedings of the National Academy of Sciences of the United States of America, 91, 8675–8679.
Zhang Y H, Bian X F, Zhang S B, Ling J, Wang Y J, Wei X Y, Fang X W. 2016. Identiifcation of a novel gain-of-function mutant allele, slr1-d5, of rice DELLA protein. Journal of Integrative Agriculture, 15, 1441–1448.
Zhang Z, Zhang Y, Tan H, Wang Y, Li G, Liang W, Yuan Z, Hu J, Ren H, Zhang D. 2011. RICE MORPHOLOGY DETERMINANT encodes the type II formin FH5 and regulates rice morphogenesis. The Plant Cell, 23, 681–700.
Zhao L, Tan L, Zhu Z, Xiao L, Xie D, Sun C. 2015. PAY1 improves plant architecture and enhances grain yield in rice. The Plant Journal, 83, 528–536.
Zheng M, Wang Y, Wang Y, Wang C, Ren Y, Lv J, Peng C, Wu T, Liu K, Zhao S, Liu X, Guo X, Jiang L, Terzaghi W, Wan J. 2015. DEFORMED FLORAL ORGAN1 (DFO1) regulates floral organ identity by epigenetically repressing the expression of OsMADS58 in rice (Oryza sativa). New Phytologist, 206, 1476–1490.
Zhou B, Lin J Z, Peng D, Yang Y Z, Guo M, Tang D Y, Tan X, Liu X M. 2017. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). Plant Science, 254, 12–21.
