Phenotypic Analysis and Gene Fine Mapping of A Semi-dwarf Multi-tiller Mutant in Rice (Oryza sativa)
CHEN Li-Ping1,2,*, JIANG Jia-Huan1,2,*, ZHU Yong-Sheng1,2, ZHENG Yan-Mei1,2, LIN Qiang1,2, XIE Hong-Guang1,2, WANG Ying-Heng1,2, CAI Qiu-Hua1,2, XIE Hua-An1,2,**, ZHANG Jian-Fu1,2,**
1 Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; 2 Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural, P.R. China/ Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/ Fujian Key Laboratory of Rice Molecular Breeding/Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences & Technology/Base of South-China, National Key Laboratory of Hybrid Rice/National Rice Engineering Laboratory of China, Fuzhou 350003, China
Abstract Plant height and tiller number are important agronomic traits affecting rice (Oryza sativa) yield. Appropriate plant height and tiller number are beneficial to increase rice yield. In this study, a semi-dwarf mutant with multi-tiller, sd-fh7185 (semi-dwarf from Fuhui 7185), was screened from the mutant library of indica restorer line 'Fuhui 7185' (FH7185) with chemical mutating of 0.1% ethylmethylsulfone (EMS). The investigated and analyzed results showed that the plant height of sd-fh7185 decreased significantly at seedling stage, tillering stage and maturity stage compared with wild type FH7185 (P<0.01), the decrease of plant height was mainly caused by the shortening of panicle and the first internode, and sd-fh7185 was controlled by a single recessive nuclear gene located on chromosome 3 (Chr. 3) in rice. Map-based cloning results indicated that the target gene, sd-fh7185, was finally fine-mapped within a physical interval of about 120 kb between InDel markers ID73 and GH25 on Chr. 3. The target region contained 14 predicted functional genes, one of which was a documented dwarf multi-tiller gene tensinte branched 1 (OsTB1)/fine cuml 1 (FC1) (MSU-RGAP locus LOC_Os03g49880) in rice. The sequencing results revealed a single base substitution from C (FH7185, wild type, WT) to T (sd-fh7185) occurred at position 439 bp of the exon of LOC_Os03g49880 in sd-fh7185, which resulted in a premature termination, and the length of encoded product was shortened from 388 amino acids (WT) to 146 amino acids (sd-fh7185) with changed function. Summarily, sd-fh7185 was a newly identified allele of OsTB1/FC1 differed from previously reported fc1-1 and fc1-2, which enriched the semi-dwarf and multi-tillering gene resources in rice, and the results provide informative references for both the dissection of molecular mechanism and rice morphology breeding in rice.
CHEN Li-Ping,JIANG Jia-Huan,ZHU Yong-Sheng, et al. Phenotypic Analysis and Gene Fine Mapping of A Semi-dwarf Multi-tiller Mutant in Rice (Oryza sativa)[J]. 农业生物技术学报, 2023, 31(1): 15-24.
[1] 方福平, 程式华. 2009. 论中国水稻生产能力[J]. 中国水稻科学, 23(6): 559-566. (Fang F P, Cheng S H.2009. Rice production capacity in China[J]. Chinese Journal of Rice Science, 23(6): 559-566.) [2] 孔会利, 刘文俊, 王令强, 等. 2007. 水稻株高QTL Qph1的精细定位[J]. 华中农业大学学报, 31(3): 265-269. (Kong H Y, Liu W J, Wang L Q, et al.2007. Fine mapping of plant height QTL Qph1 in rice[J]. Journal of Huazhong Agricultal University, 31(3): 265-269.) [3] 裘霖琳, 刘窍, 付亚萍, 等. 2022. 水稻矮化小穗基因DSP2 的鉴定与克隆[J]. 中国水稻科学, 2022, 36(2): 150-158. (Qiu L L, Liu Q, Fu Y P, et al.2022. Identification and gene cloning of DSP2 in rice (Oryza sativa L.)[J]. Chinese Journal of Rice Science, 36(2): 150-158.) [4] 周峰. 2014. 水稻矮化多分蘖基因DWARF53的图位克隆和功能研究[D]. 博士学位论文, 南京农业大学, 导师: 万建民, pp. 100-101. (Zhou F.2014. Positional cloning and functional analysis of a high-tillering dwarf gene DWARF53 in rice (Oryza sativa L.)[D]. Thesis for M.S., Nanjing Agriculture University, Supervisor: Wan J M, pp. 100-101.) [5] Chen L P, Zhao Y, Xu S H, et al.2018. OsMADS57 together with OsTB1 coordinates transcription of its target OsWRKY94 and D14 to switch its organogenesis to defense for cold adaptation in rice[J]. New Phytologist, 218(1): 219-231. [6] Fang Z M, Ji Y Y, Hu J, et al.2020. Strigolactones and brassinosteroids antagonistically regulate the stability of the D53-OsBZR1 complex to determine FC1 expression in rice tillering[J]. Molecular Plant, 13(4): 586-597. [7] Guo S Y, Xu Y Y, Liu H H, et al.2013. The interaction between OsMADS57 and OsTB1 modulates rice tillering via 'DWARF14'[J]. Nature Communications, 4(3): 1566. [8] Hedden P.2003. The genes of the green revolution[J]. Research Focus, 19(1): 5-9. [9] Itoh H, Ueguchi-Tanaka M, Sakamoto T, et al.2002. Modification of rice plant height by suppressing the height-controlling gene, D18, in rice[J]. Breeding Science, 52(3): 215-218. [10] Itoh H, Tatsumi T, Sakamoto T, et al.2004. A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase[J]. Plant Molecular Biology, 54(4): 533-547. [11] Li H, Jiang L, Youn J H, et al.2013. A comprehensive genetic study reveals a crucial role of CYP90D2/D2 in regulating plant architecture in rice (Oryza sativa)[J]. New Phytologist, 200(4): 1076-1088. [12] Li J, Jiang J F, Qian Q, et al.2011. Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation[J]. The Plant Cell, 23(2): 628-640. [13] Liu C, Zheng S, Gui J S, et al.2018. Shortened basal internodes encodes a gibberellin 2-oxidase and contributes to lodging resistance in rice[J]. Molecular Plant, 11: 288-299. [14] Liu L H, Ren M M, Peng P, et al.2021. MIT1, encoding a 15-cis-ζ-carotene isomerase, regulates tiller number and stature in rice[J]. Journal of Genetics and Genomics, 48(1): 88-91. [15] Liu X, Hu Q L, Yan J J, et al.2020. ζ-carotene isomerase suppresses tillering in rice through the coordinated biosynthesis of strigolactone and abscisic acid[J]. Molecular Plant, 13(12): 1784-1801. [16] Mccouch S R, Kochert G, Yu Z H, et al.1988. Molecular mapping of rice chromosome[J]. Theoretical and Applied Genetics, 76(6): 815-829. [17] Minakuchi K, Kameoka H, Yasuno N, et al.2010. FINE CUML1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant Cell Physiology, 51(7): 1127-1135. [18] Sakamoto T, Morinaka Y, Ohnishi T, et al.2005. Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice[J]. Nature Biotechnology, 24(1): 105-109. [19] Sasaki A, Ashikari M, Ueguchi-Tanaka M, et al.2002. A mutant gibberellin-synthesis gene in rice[J]. Nature, 416: 701-702. [20] Takeda T, Suwa Y, Suzuki M, et al.2003. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal, 33(3): 513-520. [21] Ueguchi-Tanaka M, Fujisawa Y, Kobayashi M, et al.2000. Rice dwarf mutant d1, which is defective in the α-subunit of the heterotrimeric G protein, affects gibberellin signal transduction[J]. Proceedings of the National Academy of Sciences of the USA, 97(21): 11638-11643. [22] Wang B, Smith S M, Li J Y.2018. Genetic regulation of shoot architecture[J]. Annual Review of Plant Biology, 69(1): 437-468. [23] Wang F, Han T W, Song Q X, et al.2020a. The rice circadian clock regulates tiller growth and panicle development through strigolactone signaling and sugar sensing[J]. The Plant Cell, 32(10): 3124-3138. [24] Wang Y X, Shang L G, Yu H, et al.2020b. A strigolactone biosynthesis gene contributed to the green revolution in rice[J]. Molecular Plant, 13(6): 923-932. [25] Wu T, Shen Y, Zheng M, et al.2014. Gene SGL, encoding a kinesin-like protein with transactivation activity, is involved in grain length and plant height in rice[J]. Plant Cell Reports, 33(2): 235-244. [26] Yamamuro C, Ihara Y, Wu X, et al.2000. Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint[J]. The Plant Cell, 12(9): 1591-1606. [27] Yano K, Ookawa T, Aya K, et al.2015. Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism[J]. Molecular Plant, 8(2): 303-314. [28] Yao X, Ma H, Wang J, et al.2007. Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa[J]. Journal of Integrative Plant Biology, 49(6): 885-897. [29] Zhang L, Yu H, Ma B.et al.2017. A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice[J]. Nature Communications, 8: 14789. [30] Zhang Q F, Shen B Z, Dai X K, et al.1994. Using bulked extremes and recessive class to map genes for photoperiod-sensitive genic male sterility in rice[J]. Proceedings of the National Academy of Sciences of the USA, 91(18): 8675-8679. [31] Zheng J S, Hong K, Zeng L J, et al.2020. Karrikin signaling acts parallel to and additively with strigolactone signaling to regulate rice mesocotyl elongation in darkness[J]. The Plant Cell, 32(9): 2780-2805. [32] Zhou F, Lin Q B, Zhu L H.et al.2013. D14-SCFD3-dependent degradation of D53 regulates strigolactone signalling[J]. Nature, 504(7480): 406-410.