水稻窄长粒突变体nlg1的筛选及候选基因鉴定

doi:10.16288/j.yczz.24-329

[an error occurred while processing this directive]

Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (6): 672-680.doi: 10.16288/j.yczz.24-329

• Research Article • Previous Articles Next Articles

Genetic analysis and identification of candidate genes for a narrow and long grain mutant (nlg1) in rice

Nian Guo¹(), Chenjie Wang¹, Zhao Li¹, Nannan Han¹, Chen Zhou¹, Kaiying Wang¹, Ke Huang², Yongqing Pan²^,³, Yingjie Li²(), Yunhai Li²()

1. School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
2. Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
3. University of Chinese Academy of Sciences, Beijing 100039, China

Received:2024-11-14 Revised:2024-12-29 Online:2025-06-20 Published:2025-02-21
Contact: Yingjie Li, Yunhai Li E-mail:1243323954@qq.com;liyingjie@genetics.ac.cn;yhli@genetics.ac.cn
Supported by:
National Key Research and Development Program of China(2021YFF1000202);National Key Research and Development Program of China(2022YFF1002903)

Abstract

Abstract:

Grain size is one of the components that determine the rice yield. Exploring more key genes that regulating grain size and analyzing their molecular mechanisms are of great importance for precision breeding of rice. In this study, we screened a mutant nlg1(narrow and long grain 1) with narrow and long grains by mutagenizing the japonica rice variety ZH11 with EMS. Observation and statistical analysis of the outer surface of the mature glume of nlg1 by scanning electron microscopy revealed an increased number of longitudinal cells and a decreased number of transverse cells, along with a reduction in the width of transverse cells. These findings suggest that NLG1 may regulate grain size by simultaneously influencing the proliferation and expansion of lemma cells. The candidate gene was cloned by genome resequencing combined with MutMap analysis method. The results showed that the candidate gene of LOC_Os09g27590 was the previous reported gene, GS9, which encodes a protein with unknown domains. In the nlg1 mutant, a base C was inserted in the first exon of the candidate gene of LOC_Os09g27590, causing a frameshift mutation that leads to premature termination of protein translation. Further genetic complementation experiments showed that NLG1 rescued the phenotype of the nlg1 mutant. Therefore, this study identifies a novel GS9 allele mutation, and further dissection of its molecular regulatory networks in grain size control can provides a theoretical support and genetic resources for precise rice breeding.

Key words: rice, grain size, MutMap, GS9

Nian Guo, Chenjie Wang, Zhao Li, Nannan Han, Chen Zhou, Kaiying Wang, Ke Huang, Yongqing Pan, Yingjie Li, Yunhai Li. Genetic analysis and identification of candidate genes for a narrow and long grain mutant (nlg1) in rice[J]. Hereditas(Beijing), 2025, 47(6): 672-680.

Figures/Tables 6

Table 1

Fig. 1

Fig. 2

Table 2

Fig. 3

Fig. 4

References 38

[1]	Takeda S, Matsuoka M. Genetic approaches to crop improvement: responding to environmental and population changes. Nat Rev Genet, 2008, 9(6): 444-457. pmid: 18475268
[2]	Yuan LP. Developing hybrid rice to ensure food security. Hybrid Rice, 2010, 25(S1): 1-2.
	袁隆平. 发展杂交水稻保障粮食安全. 杂交水稻, 2010, 25(S1): 1-2.
[3]	Ren DY, Ding CQ, Qian Q. Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing), 2023, 68(3): 314-350. pmid: 36710151
[4]	Lan JS, Zhuang H. Advances in the molecular mechanism of rice plant type. Chin J Rice Sci, 2023, 37(5): 449-458.
	兰金松, 庄慧. 水稻株型的分子机理研究进展. 中国水稻科学, 2023, 37(5): 449-458.
[5]	Huang Y, Hu Y, Fu XD, Xing YZ. Functional genes for grain yield related traits and their application in rice breeding. Chin Bull Life Sci, 2016, 28(10): 1147-1155.
	黄勇, 胡勇, 傅向东, 邢永忠. 水稻产量性状的功能基因及其应用. 生命科学, 2016, 28(10): 1147-1155.
[6]	Che RH, Tong HN, Shi BH, Liu YQ, Fang SR, Liu DP, Xiao YH, Hu B, Liu LC, Wang HR, Zhao MF, Chu CC. Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nat Plants, 2015, 2: 15195. pmid: 27250747
[7]	Duan PG, Ni S, Wang JM, Zhang BL, Xu R, Wang YX, Chen HQ, Zhu XD, Li YH. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice. Nat Plants, 2015, 2: 15203. pmid: 27250749
[8]	Hu J, Wang YX, Fang YX, Zeng LJ, Xu J, Yu HP, Shi ZY, Pan JJ, Zhang D, Kang SJ, Zhu L, Dong GJ, Guo LB, Zeng DL, Zhang GH, Xie LH, Xiong GS, Li JY, Qian Q. A rare allele of GS2 enhances grain size and grain yield in rice. Mol Plant, 2015, 8(10): 1455-1465. pmid: 26187814
[9]	Li SC, Gao FY, Xie KL, Zeng XH, Cao Y, Zeng J, He ZS, Ren Y, Li WB, Deng QM, Wang SQ, Zheng AP, Zhu J, Liu HN, Wang LX, Li P. The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice. Plant Biotechnol J, 2016, 14(11): 2134-2146. pmid: 27107174
[10]	Segami S, Kono I, Ando T, Yano M, Kitano H, Miura K, Iwasaki Y. Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice. Rice (N Y), 2012, 5(1): 4. pmid: 24764504
[11]	Sunohara H, Kawai T, Shimizu-Sato S, Sato Y, Sato K, Kitano H. A dominant mutation of TWISTED DWARF 1 encoding an alpha-tubulin protein causes severe dwarfism and right helical growth in rice. Genes Genet Syst, 2009, 84(3): 209-218. pmid: 19745569
[12]	Si LZ, Chen JY, Huang XH, Gong H, Luo JH, Hou QQ, Zhou TY, Lu TT, Zhu JJ, Shangguan YY, Chen EW, Gong CX, Zhao Q, Jing YF, Zhao Y, Li Y, Cui LL, Fan DL, Lu YQ, Weng QJ, Wang YC, Zhan QL, Liu KY, Wei XH, An K, An G, Han B. OsSPL13 controls grain size in cultivated rice. Nat Genet, 2016, 48(4): 447-456. pmid: 26950093
[13]	Hu JH, Huang LY, Chen GL, Liu H, Zhang YS, Zhang R, Zhang SL, Liu JT, Hu QY, Hu FY, Wang W, Ding Y. The elite alleles of OsSPL4 regulate grain size and increase grain yield in rice. Rice (N Y), 2021, 14(1): 90. pmid: 34727228
[14]	Yuan H, Qin P, Hu L, Zhan SJ, Wang SF, Gao P, Li J, Jin MY, Xu ZY, Gao Q, Du AP, Tu B, Chen WL, Ma BT, Wang YP, Li SG. OsSPL18 controls grain weight and grain number in rice. J Genet Genomics, 2019, 46(1): 41-51. pmid: 30737149
[15]	Wang SK, Wu K, Yuan QB, Liu XY, Liu ZB, Lin XY, Zeng RZ, Zhu HT, Dong GJ, Qian Q, Zhang GQ, Fu XD. Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet, 2012, 44(8): 950-954. pmid: 22729225
[16]	Qin MM, Zhang Y, Yang YM, Miao CB, Liu SK. Seed-specific overexpression of SPL12 and IPA1 improves seed dormancy and grain size in rice. Front Plant Sci, 2020, 11: 532771. pmid: 33013960
[17]	Zhang XF, Yang CY, Lin HX, Wang JW, Xue HW. Rice SPL12 coevolved with GW5 to determine grain shape. Sci Bull (Beijing), 2021, 66(23): 2353-2357. pmid: 36654120
[18]	Yan Y, Wei MX, Li Y, Tao H, Wu HY, Chen ZF, Li C, Xu JH. MiR529a controls plant height, tiller number, panicle architecture and grain size by regulating SPL target genes in rice (Oryza sativa L.). Plant Sci, 2021, 302: 110728. pmid: 33288029
[19]	Yue EK, Li C, Li Y, Liu Z, Xu JH. MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa). Plant Mol Biol, 2017, 94(4-5): 469-480. pmid: 28551765
[20]	Huang Y, Bai XF, Cheng NN, Xiao JH, Li XH, Xing YZ. Wide Grain 7 increases grain width by enhancing H3K4me3 enrichment in the OsMADS1 promoter in rice (Oryza sativa L.). Plant J, 2020, 102(3): 517-528. pmid: 31830332
[21]	Liu Q, Han RX, Wu K, Zhang JQ, Ye YF, Wang SS, Chen JF, Pan YJ, Li Q, Xu XP, Zhou JW, Tao DY, Wu YJ, Fu XD. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat Commun, 2018, 9(1): 852. pmid: 29487282
[22]	Zuo ZW, Zhang ZH, Huang DR, Fan YY, Yu SB, Zhuang JY, Zhu YJ. Control of thousand-grain weight by OsMADS56 in rice. Int J Mol Sci, 2021, 23(1): 125. pmid: 35008551
[23]	Zhan PL, Ma SP, Xiao ZL, Li FP, Wei X, Lin SJ, Wang XL, Ji Z, Fu Y, Pan JH, Zhou M, Liu Y, Chang ZY, Li L, Bu SH, Liu ZP, Zhu HT, Liu GF, Zhang GQ, Wang SK. Natural variations in grain length 10 (GL10) regulate rice grain size. J Genet Genomics, 2022, 49(5): 405-413. pmid: 35151907
[24]	Zhang Y, Yu HP, Liu J, Wang W, Sun J, Gao Q, Zhang YH, Ma DR, Wang JY, Xu ZJ, Chen WF. Loss of function of OsMADS34 leads to large sterile lemma and low grain yield in rice (Oryza sativa L.). Mol Breed, 2016, 36(11): 147.
[25]	Yu XQ, Xia SS, Xu QK, Cui YJ, Gong M, Zeng DL, Zhang Q, Shen L, Jiao GA, Gao ZY, Hu J, Zhang GH, Zhu L, Guo LB, Ren DY, Qian Q. ABNORMAL FLOWER AND GRAIN 1 encodes OsMADS6 and determines palea identity and affects rice grain yield and quality. Sci China Life Sci, 2020, 63(2): 228-238. pmid: 31919631
[26]	Lan J, Lin QB, Zhou CL, Ren YK, Liu X, Miao R, Jing RN, Mou CL, Nguyen T, Zhu XJ, Wang Q, Zhang X, Guo XP, Liu SJ, Jiang L, Wan JM. Small grain and semi-dwarf 3, a WRKY transcription factor, negatively regulates plant height and grain size by stabilizing SLR1 expression in rice. Plant Mol Biol, 2020, 104(4-5): 429-450. pmid: 32808190
[27]	Tian XJ, He ML, Mei EY, Zhang BW, Tang JQ, Xu M, Liu JL, Li XF, Wang ZY, Tang WQ, Guan QJ, Bu QY. WRKY53 integrates classic brassinosteroid signaling and the mitogen-activated protein kinase pathway to regulate rice architecture and seed size. Plant Cell, 2021, 33(8): 2753-2775. pmid: 34003966
[28]	Xiang JS, Tang S, Zhi H, Jia GQ, Wang HJ, Diao XM. Loose Panicle1 encoding a novel WRKY transcription factor, regulates panicle development, stem elongation, and seed size in foxtail millet [Setaria italica (L.) P. Beauv.]. PLoS One, 2017, 12(6): e0178730. pmid: 28570666
[29]	Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H, Obara T, Oikawa K, Utsushi H, Kanzaki E, Mitsuoka C, Natsume S, Kosugi S, Kanzaki H, Matsumura H, Urasaki N, Kamoun S, Terauchi R. MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol, 2015, 33(5): 445-449. pmid: 25798936
[30]	Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol, 2012, 30(2): 174-178. pmid: 22267009
[31]	Huang LJ, Hua K, Xu R, Zeng DL, Wang RC, Dong GJ, Zhang GZ, Lu XL, Fang N, Wang DK, Duan PG, Zhang BL, Liu ZP, Li N, Luo YH, Qian Q, Yao SG, Li YH. The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice. Plant Cell, 2021, 33(4): 1212-1228. pmid: 33693937
[32]	Lyu J, Wang DK, Duan PG, Liu YP, Huang K, Zeng DL, Zhang LM, Dong GJ, Li YJ, Xu R, Zhang BL, Huang XH, Li N, Wang YC, Qian Q, Li YH. Control of grain size and weight by the GSK2-LARGE1/OML4 pathway in rice. Plant Cell, 2020, 32(6): 1905-1918. pmid: 32303659
[33]	Zhao DS, Li QF, Zhang CQ, Zhang C, Yang QQ, Pan LX, Ren XY, Lu J, Gu MH, Liu QQ. GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nat Commun, 2018, 9(1): 1240. pmid: 29588443
[34]	Yang C, Shen WJ, He Y, Tian ZH, Li JX. OVATE family protein 8 positively mediates brassinosteroid signaling through interacting with the GSK3-like kinase in rice. PLoS Genet, 2016, 12(6): e1006118. pmid: 27332964
[35]	Yu Y, He RR, Yang L, Feng YZ, Xue J, Liu Q, Zhou YF, Lei MQ, Zhang YC, Lian JP, Chen YQ. A transthyretin- like protein acts downstream of miR397 and LACCASE to regulate grain yield in rice. Plant Cell, 2024, 36(8): 2893-2907. pmid: 38735686
[36]	Li N, Xu R, Li YH. Molecular networks of seed size control in plants. Annu Rev Plant Biol, 2019, 70: 435-463. pmid: 30795704
[37]	Dang S, Zhang ZY, Chen DY, Yuan MH. Research progress of different plant-panicle types of rice varieties. J Anhui Agric Sci, 2019, 47(6): 14-15+19.
	党姝, 张振宇, 陈殿元, 元明浩. 不同株穗型水稻品种研究进展. 安徽农业科学, 2019, 47(6): 14-15+19.
[38]	Zhao DS, Liu JY, Ding AQ, Zhang T, Ren XY, Zhang L, Li QF, Fan XL, Zhang CQ, Liu QQ. Improving grain appearance of erect-panicle japonica rice cultivars by introgression of the null gs9 allele. J Integr Agric, 2021, 20(8): 2032-2042.

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

引物名称	引物序列(5′→3′)	用途
nlg1seq-F	CTCCTCACTCATCCTACTC	鉴定nlg1突变位点引物
nlg1seq-R	AAGAAACTGTTGCCTTTGCTCT	鉴定nlg1突变位点引物
COM-F	TGACCATGATTACGAATTCGAGCTCCTTAAGCTCACTGACCTCAC	构建互补载体引物
COM-R	TAAAACGACGGCCAGTGCCAAGCTTTCCTGCTCTACCCTGTCTTT	构建互补载体引物
COM-JD-F	CTCCTCACTCATCCTACTC	转基因苗鉴定引物
COM-JD-R	TCGTCGTCAGCTAATCATCG	转基因苗鉴定引物

编号	染色体	物理位置	碱基变化	所在位置	基因号	测序频次	突变类型
INDEL1	Chr.9	2826399	A/AT	基因间区	/	0/8	/
SNP1	Chr.9	3547096	A/C	基因间区	/	0/7	/
SNP2	Chr.9	15786577	G/A	5'UTR	LOC_Os05g39250	0/24	/
INDEL2	Chr.9	16691171	G/GC	外显子	LOC_Os09g27590	0/27	移码突变
SNP3	Chr.9	18187015	T/C	基因上游	LOC_Os09g29980	0/15	/
INDEL3	Chr.9	22586699	A/AAC	基因上游	LOC_Os09g39330	0/20	/
INDEL4	Chr.9	23212674	T/TG	基因上游	LOC_Os09g34310	0/5	/

Genetic analysis and identification of candidate genes for a narrow and long grain mutant (nlg1) in rice

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 6

References 38

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Zhanchun Wang, Guitao Zhong, Beibei Zhang, Yilin Xie, Dingzhong Tang, Wei Wang. Research advances in rice blast resistance genes [J]. Hereditas(Beijing), 2025, 47(5): 533-545.
[2]	Jiawen Ma, Xinle Liang. Analysis of structure and function of phage community occurring in the abnormal fermentation of vinegar mash through virome sequencing [J]. Hereditas(Beijing), 2025, 47(4): 489-498.
[3]	Yueyang Wu, Xiaoyan Zhou, Yufeng Wu, Ju Huang. Effects of functional defects in the NMD pathway on rice phenotype and transcriptome [J]. Hereditas(Beijing), 2024, 46(7): 540-551.
[4]	Zhong Bian, Dongping Cao, Wenshu Zhuang, Shuwei Zhang, Qiaoquan Liu, Lin Zhang. Revelation of rice molecular design breeding: the blend of tradition and modernity [J]. Hereditas(Beijing), 2023, 45(9): 718-740.
[5]	Xiangdong Liu, Jinwen Wu, Zijun Lu, Muhammad Qasim Shahid. Autotetraploid rice: challenges and opportunities [J]. Hereditas(Beijing), 2023, 45(9): 781-792.
[6]	Zhenwu Zheng, Hongyuan Zhao, Xiaoya Liang, Yijun Wang, Chihang Wang, Gaoyan Gong, Jinyan Huang, Guiquan Zhang, Shaokui Wang, Zupei Liu. qGL3.4 controls kernel size and plant architecture in rice [J]. Hereditas(Beijing), 2023, 45(9): 835-844.
[7]	Mingjiang Chen, Guifu Liu, Yeqing Xiao, Hong Yu, Jiayang Li. Breeding of ZhongKeFaZaoGeng1 by molecular design [J]. Hereditas(Beijing), 2023, 45(9): 829-834.
[8]	Xiaoping Lian, Guangfu Huang, Yujiao Zhang, Jing Zhang, Fengyi Hu, Shilai Zhang. The discovery and utilization of favorable genes in Oryza longistaminata [J]. Hereditas(Beijing), 2023, 45(9): 765-780.
[9]	Yongqiang Liu, Weiwei Li, Xinyu Liu, Chengcai Chu. Molecular mechanism of tillering response to nitrogen in rice [J]. Hereditas(Beijing), 2023, 45(5): 367-378.
[10]	Shan Li, Yunzhi Huang, Xueying Liu, Xiangdong Fu. Genetic improvement of nitrogen use efficiency in crops [J]. Hereditas(Beijing), 2021, 43(7): 629-641.
[11]	Changquan Zhang, Linhao Feng, Minghong Gu, Qiaoquan Liu. Progress on inheritance and gene cloning for rice grain quality in Jiangsu province [J]. Hereditas(Beijing), 2021, 43(5): 425-441.
[12]	Cailin Wang, Yadong Zhang, Chunfang Zhao, Xiaodong Wei, Shu Yao, Lihui Zhou, Zhen Zhu, Tao Chen, Qingyong Zhao, Ling Zhao, Kai Lu, Wenhua Liang. Inheritance and breeding of japonica rice with good eating quality in Jiangsu province [J]. Hereditas(Beijing), 2021, 43(5): 442-458.
[13]	Hang Dai, Yan Li, Shunchun Liu, Lei Lin, Juanyan Wu, Zhijie Zhang, Qichun Peng, Nan Li, Xiangqian Zhang. Effect of extensin-like OsPEX1 on pollen fertility in rice [J]. Hereditas(Beijing), 2021, 43(3): 271-279.
[14]	Lingyue Yan, Haojian Zhang, Yuqing Zheng, Yunqi Cong, Citao Liu, Fan Fan, Cheng Zheng, Guilong Yuan, Gen Pan, Dingyang Yuan, Meijuan Duan. Transcription factor OsMADS25 improves rice tolerance to cold stress [J]. Hereditas(Beijing), 2021, 43(11): 1078-1087.
[15]	Yali Hu, Rui Dai, Yongxin Liu, Jingying Zhang, Bin Hu, Chengcai Chu, Huaibo Yuan, Yang Bai. Analysis of rice root bacterial microbiota of Nipponbare and IR24 [J]. Hereditas(Beijing), 2020, 42(5): 506-518.