Progress in Regulation of Important Agronomic Traits by Semi-Dwarf Gene sd1 in Rice

doi:10.16819/j.1001-7216.2025.231104

Abstract

Abstract:

The cultivation and popularization of semi-dwarf varieties have promoted the “Green Revolution” of rice. The semi-dwarf gene sd1 in rice is a key gene responsible for gibberellin synthesis, which decreases plant height, increases harvest index. The application of sd1 addressed the problem of high yield and lodging under conditions of increased nitrogen fertilizer application. In this paper, the isolation and functional analysis of the sd1 gene were reviewed, the differences in important agronomic traits among different haplotypes of sd1 were analyzed, and the mechanisms by which the sd1 gene regulated key agronomic traits such as growth period, plant height, number of panicles per plant, yield per plant, lodging resistance, seed dormancy, and nitrogen use efficiency were reviewed. The effect of the sd1 gene on rice yield was discussed, along with the application of gene editing technology to generate sd1 mutations for the rapid improvement of rice varieties. Moreover, the potential application of the sd1 gene was anticipated.

Key words: dwarfing breeding, sd1, Oryza sativa, semi-dwarf

摘要：

半矮秆品种的培育和推广推动了水稻“绿色革命”。半矮秆基因sd1是参与赤霉素合成的关键基因。该位点的变异降低了株高，提高了收获指数，解决了在增施氮肥条件下高产与倒伏之间的矛盾。本文回顾了sd1基因的分离与功能解析，分析了sd1不同单体型间的重要农艺性状的差异，综述了sd1基因调控对包括生育期、株高、单株穗数、单株产量、抗倒伏、种子休眠和氮肥利用率等重要农艺性状的作用机理，讨论了sd1基因对水稻产量的影响和利用基因编辑技术创制sd1变异定向快速改良水稻品种，并对sd1基因的应用进行了展望。

关键词: 矮化育种, sd1, 水稻, 半矮秆

ZHANG Fengyong, YING Xiaoping, ZHANG Jian, YANG Longwei, YING Jiezheng. Progress in Regulation of Important Agronomic Traits by Semi-Dwarf Gene sd1 in Rice[J]. Chinese Journal OF Rice Science, 2025, 39(1): 24-32.

张丰勇, 应晓平, 张健, 杨隆维, 应杰政. 半矮秆基因sd1调控水稻重要农艺性状的研究进展[J]. 中国水稻科学, 2025, 39(1): 24-32.

Figures/Tables 3

Fig. 1. Functional mechanisms of sd1 gene regulating important agronomic traits in rice

Table 1. Haplotype of the SD1 gene in RFGP data

单倍型 Haplotype	SNP1 (38382762)	SNP2 (38382764)	SNP3 (38383144)	SNP4 (38383221)	SNP5 (38385057)	SNP6 (38385199)	Aus	Bas	XI	GJ	Admix	合计Total
Hap_1(NIP)	C	A	T	C	A	G	1	33	27	522	18	601
Hap_2	C	G	T	T	G	G	33	0	585	0	15	633
Hap_3	C	G	T	C	G	G	80	1	121	0	7	209
Hap_4	C	G	T	C	G	A	0	0	117	0	1	118
Hap_5	-	-	-	T	G	G	0	0	78	8	3	89
Hap_6	C	G	T	T	G	G	2	0	71	0	3	76

Fig. 2. Comparison of agronomic traits among different haplotypes of SD1 gene including plant height, panicle length, days to heading, grain length, grain width, and thousand-grain weight The same letter on the column indicates that difference between the haplotypes was not significant at the 0.05 level.

References 50

[1]	Khan M H, Dar Z A, Dar S A. Breeding strategies for improving rice yield: A review[J]. Agricultural Sciences, 2015, 6(5): 467-478.
[2]	Hedden P. The genes of the Green Revolution[J]. Trends in Genetic, 2003, 19(1): 5-9.
[3]	Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush G S, Kitano H, Matsuoka M. Green revolution: A mutant gibberellin-synthesis gene in rice: New insight into the rice variant that helped to avert famine over thirty years ago[J]. Nature, 2002, 416(6882): 701-702.
[4]	Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y. Positional cloning of rice semidwarfing gene, sd-1: Rice "Green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis[J]. DNA Research, 2002, 9(1): 11-17.
[5]	Khush G S. Green revolution: preparing for the 21st century[J]. Genome, 1999, 42(4): 646-655.
[6]	Khush G S. Modern varieties-Their real contribution to food supply and equity[J]. GeoJournal, 1995, 35(3): 275-284.
[7]	Xue H D, Zhang Y Z, Xiao G H. Neo-gibberellin Signaling: Guiding the Next Generation of the Green Revolution[J]. Trends in Plant Science, 2020, 25(6): 520-522.
[8]	Vriet C, Russinova E, Reuzeau C. Boosting crop yields with plant steroids[J]. Plant Cell, 2012, 24(3): 842-857.
[9]	Peng S, Cassman K G, Virmani S S, Sheehy J, Khush G S. Yield potential trends of tropical rice since the release of IR8 and the challenge of increasing rice yield potential[J]. Crop Science, 1999, 39(6): 1552-1559.
[10]	Peng J R, Richards D E, Hartley N M, Murphy G P, Devos K M, Flintham J E, Beales J, Fish L J, Worland A J, Pelica F, Sudhakar D, Christou P, Snape J W, Gale M D, Harberd N P. Green revolution genes encode mutant gibberellin response modulators[J]. Nature, 1999, 400(6741): 256-261.
[11]	Jia X Q, Yu L Y, Tang M L, Tian D C, Yang S H, Zhang X H, Traw M B. Pleiotropic changes revealed by recovery of the semi-dwarf gene in rice[J]. Journal of Plant Physiology, 2020, 248: 153141.
[12]	Liu Q, Wu K, Wu Y, Song W, Wang S, Fu X. Beyond the Green Revolution: Improving crop productivity and sustainability by modulating plant growth-metabolic coordination[J]. Molecular Plant, 2022, 15(4): 573-576.
[13]	Fleet C M, Sun T P. A DELLAcate balance: The role of gibberellin in plant morphogenesis[J]. Current Opinion in Plant Biology, 2005, 8(1): 77-85.
[14]	Koboyashi M, Yamaguchi I, Murofushi N, Ota Y, Takahashi N. Fluctuation and localization of endogenous gibberellins in rice[J]. Agricultural and Biological Chemistry, 1988, 52(5): 1189-1194.
[15]	Varbanova M, Yamaguchi S, Yang Y, Mckelvey K, Hanada A, Borochov R, Yu F, Jikumaru Y, Ross J, Cortes D, Ma C J, Noel J P, Mander L, Shulaev V, Kamiya Y, Rodermel S, Weiss D, Pichersky E. Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2[J]. Plant Cell, 2007, 19(1): 32-45.
[16]	Spielmeyer W, Ellis M, Chandler P. Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene[J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99(13): 9043-9048.
[17]	Wu B, Hu W, Ayaad M, Liu H B, Xing Y Z. Intragenic recombination between two non-functional-alleles produced a functional allele in a tall recombinant inbred line in rice[J]. Plos ONE, 2017, 12(12): e0190116.
[18]	Wang C C, Yu H, Huang J, Wang W S, Faruquee M, Zhang F, Zhao X Q, Fu B Y, Chen K, Zhang H L, Tai S S, Wei C C, Mcnally K L, Alexandrov N, Gao X Y, Li J Y, Li Z K, Xu J L, Zheng T Q. Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0[J]. Plant Biotechnology Journal, 2020, 18(1): 14-16.
[19]	Asano K, Takashi T, Miura K, Qian Q, Kitano H, Matsuoka M, Ashikari M. Genetic and molecular analysis of utility of sd1 alleles in rice breeding[J]. Breeding Science, 2007, 57(1): 53-58.
[20]	Asano K, Yamasaki M, Takuno S, Miura K, Katagiri S, Ito T, Doi K, Wu J Z, Ebana K, Matsumoto T, Innan H, Kitano H, Ashikari M, Matsuoka M. Artificial selection for a green revolution gene during japonica rice domestication[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(27): 11034-11039.
[21]	Yu Y, Hu X, Zhu Y, Mao D. Re-evaluation of the rice ‘Green Revolution’ gene: The weak allele SD1-EQ from japonica rice may be beneficial for super indica rice breeding in the post-Green Revolution era[J]. Molecular Breeding, 2020, 40(9).
[22]	Zentella R, Zhang Z L, Park M, Thomas S G, Endo A, Murase K, Fleet C M, Jikumaru Y, Nambara E, Kamiya Y, Sun T P. Global analysis of DELLA direct targets in early gibberellin signaling in Arabidopsis[J]. Plant Cell, 2007, 19(10): 3037-3057.
[23]	Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J. slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8[J]. Plant Cell, 2001, 13(5): 999-1010.
[24]	Willige B C, Ghosh S, Nill C, Zourelidou M, Dohmann E M N, Maier A, Schwechheimer C. The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis[J]. Plant Cell, 2007, 19(4): 1209-1220.
[25]	Wu K, Wang S S, Song W Z, Zhang J Q, Wang Y, Liu Q, Yu J P, Ye Y F, Li S, Chen J F, Zhao Y, Wang J, Wu X K, Wang M Y, Zhang Y J, Liu B M, Wu Y J, Harberd N P, Fu X D. Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice[J]. Science, 2020, 367(6478): 641.
[26]	Liao Z G, Yu H, Duan J B, Yuan K, Yu C J, Meng X B, Kou L Q, Chen M J, Jing Y H, Liu G F, Smith S M, Li J Y. SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice[J]. Nature Communications, 2019, 10.
[27]	Su S, Hong J, Chen X F, Zhang C Q, Chen M J, Luo Z J, Chang S W, Bai S X, Liang W Q, Liu Q Q, Zhang D B. Gibberellins orchestrate panicle architecture mediated by DELLA-KNOX signalling in rice[J]. Plant Biotechnology Journal, 2021, 19(11): 2304-2318.
[28]	Ye H, Beighley D H, Feng J H, Gu X Y. Genetic and physiological characterization of two clusters of quantitative trait loci associated with seed dormancy and plant height in rice[J]. Genes Genomes Genetics, 2013, 3(2): 323-331.
[29]	Ye H, Feng J, Zhang L, Zhang J, Mispan M, Cao Z, Beighley D, Yang J, Gu X. Map-based cloning of seed dormancy1-2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice[J]. Plant Physiology, 2015, 169(3): 2152-2165.
[30]	Murai M, Hirose S, Sato S. Effects of the dwarfing gene from Dee-geo-woo-gen and others on cool temperature tolerance at flowering stage in rice[J]. Japanese Journal of Breeding, 1992, 42(4): 811-823.
[31]	徐青山, 黄晶, 孙爱军, 洪小智, 朱练峰, 曹小闯, 孔亚丽, 金千瑜, 朱春权, 张均华. 低温影响水稻发育机理及调控途径研究进展[J]. 中国水稻科学, 2022, 36(2): 118-130.
	Xu Q S, Huang J, Sun A J, Hong X Z, Zhu L F, Cao X C, Kong Y L, Jin Q Y, Zhu C Q, Zhang J H. Effects of low temperature on the growth and development of rice plants and the advance of regulation pathways[J]. Chinese Journal of Rice Science, 2022, 36(2): 118-130. (in Chinese with English abstract)
[32]	Sakata T, Oda S, Tsunaga Y, Shomura H, Kawagishi-Kobayashi M, Aya K, Saeki K, Endo T, Nagano K, Kojima M, Sakakibara H, Watanabe M, Matsuoka M, Higashitani A. Reduction of gibberellin by low temperature disrupts pollen development in in rice[J]. Plant Physiology, 2014, 164(4): 2011-2019.
[33]	Vikram P, Swamy B P M, Dixit S, Singh R, Singh B P, Miro B, Kohli A, Henry A, Singh N K, Kumar A. Drought susceptibility of modern rice varieties: An effect of linkage of drought tolerance with undesirable traits[J]. Scientific Reports, 2015, 5: 14799.
[34]	Terao T, Hirose T. Control of grain protein contents throughSEMIDWARF1 mutant alleles: sd1increases the grain protein content in Dee-geo-woo-gen but not in Reimei[J]. Molecular Genetics and Genomics, 2015, 290(3): 939-954.
[35]	Li S, Tian Y H, Wu K, Ye Y F, Yu J P, Zhang J Q, Liu Q, Hu M Y, Li H, Tong Y P, Harberd N P, Fu X D. Modulating plant growth-metabolism coordination for sustainable agriculture[J]. Nature, 2018, 560(7720): 595.
[36]	Wang C, Feng X M, Yuan Q B, Lin K X, Zhang X H, Yan L, Nan J Z, Zhang W Q, Wang R S, Wang L H, Xue Q, Yang X W, Liu Z X, Lin S Y. Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement[J]. Plant Biotechnology Journal, 2023, 21(2): 419-432.
[37]	Hu X M, Cui Y T, Dong G J, Feng A H, Wang D Y, Zhao C Y, Zhang Y, Hu J, Zeng D L, Guo L B, Qian Q. Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces[J]. Scientific Reports, 2019, 9: 19096.
[38]	李刚, 高清松, 李伟, 张雯霞, 王健, 程保山, 王迪, 徐卫军, 陈红旗, 纪剑辉. 定向敲除SD1基因提高水稻抗倒性和稻瘟病抗性[J]. 中国水稻科学, 2023, 37(4): 359-367.
	Li G, Gao Q S, Li W, Zhang W X, Wang J, Chen B S, Wang D, Gao H, Xu W J, Chen H Q, Ji J H. Directed knockout of SD1 gene improves lodging resistance and blast resistance of rice[J]. Chinese Journal of Rice Science, 2023, 37(4): 359-367. (in Chinese with English abstract)
[39]	黄先忠, 马正强. DELLA家族蛋白与植物生长发育的关系[J]. 植物生理学通讯, 2004(5): 529-532.
	Huang X Z, Ma Z Q. Progress in studies on DELLA protein family in plant growth and development[J]. Plant Physiology Communications, 2004(5): 529-532. (in Chinese with English abstract)
[40]	Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim R B, Komura T, Satoh H, Kitano H, Matsuoka M, Ashikari M. Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice[J]. Molecular Genetics and Genomics, 2009, 281(2): 223-231.
[41]	Wu Z G G, Tang D, Liu K, Miao C B, Zhuo X X, Li Y F, Tan X L, Sun M F, Luo Q, Cheng Z K. Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding[J]. Journal of Experimental Botany, 2018, 69(20): 4703-4713.
[42]	Kovi M, Zhang Y S, Yu S B, Yang G Y, Yan W H, Xing Y Z. Candidacy of a chitin-inducible gibberellin-responsive gene for a major locus affecting plant height in rice that is closely linked to Green Revolution gene sd1[J]. Theoretical and Applied Genetics, 2011, 123(5): 705-714.
[43]	刘佳欣, 吴周周, 周婵婵, 阿娜, 李漪濛, 王术. 水稻倒伏性状与抗倒途径研究进展[J]. 中国稻米, 2023 (6): 1-6.
	Liu J X, Wu Z Z, Zhou C C, A N, Li Y M, Wang S. Research progress of lodging characters and lodging resistance pathways in rice[J]. China Rice, 2023(6): 44-48. (in Chinese with English abstract)
[44]	Sun H Y, Qian Q, Wu K, Luo J J, Wang S S, Zhang C W, Ma Y F, Liu Q, Huang X Z, Yuan Q B, Han R X, Zhao M, Dong G J, Guo L B, Zhu X D, Gou Z H, Wang W, Wu Y J, Lin H X, Fu X D. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice[J]. Nature Genetics, 2014, 46(6): 652-656.
[45]	Tanokura M, Miyakawa T, Xue Y, Nakamura H, Hou F, Qin H, Fukui K, Shi X, Ito S, Miyauchi Y, Asano A, Totsuka N, Asami T. Molecular mechanism of strigolactone perception by DWARF14[J]. Acta Crystallographica a-Foundation and Advances, 2014, 70: C1062-C1062.
[46]	Sun H, Guo X, Zhu X, Gu P, Zhang W, Tao W, Wang D, Wu Y, Zhao Q, Xu G, Fu X, Zhang Y. Strigolactone and gibberellin signaling coordinately regulate metabolic adaptations to changes in nitrogen availability in rice[J]. Molecular Plant, 2023, 16(3): 588-598.
[47]	Asami T. Toward the next step to the New Green Revolution[J]. Molecular Plant, 2023, 16(5): 802-803.
[48]	Wang Y X, Shang L G, Yu H, Zeng L J, Hu J, Ni S, Rao Y C, Li S F, Chu J F, Meng X B, Wang L, Hu P, Yan J J, Kang S J, Qu M H, Lin H, Wang T, Wang Q, Hu X M, Chen H Q, Wang B, Gao Z Y, Guo L B, Zeng D L, Zhu X D, Xiong G S, Li J Y, Qian Q. A strigolactone biosynthesis gene contributed to the green revolution in rice[J]. Molecular Plant, 2020, 13(6): 923-932.
[49]	Nomura T, Arakawa N, Yamamoto T, Ueda T, Adachi S, Yonemaru J, Abe A, Takagi H, Yokoyama T, Ookawa T. Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1[J]. Plos One, 2019, 14(8).
[50]	兰金松, 庄慧. 水稻株型的分子机理研究进展[J]. 中国水稻科学, 2023, 37(5): 449-458.
	Lan J S, Zhuang H. Advances in the molecular mechanism of rice plant type[J]. Chinese Journal of Rice Science, 2023, 37(5): 449-458. (in Chinese with English abstract)