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Journal of Integrative Agriculture  2024, Vol. 23 Issue (7): 2155-2163    DOI: 10.1016/j.jia.2023.07.026
Special Issue: 水稻遗传育种Rice Genetics · Breeding · Germplasm Resources
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Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S
Bin Lei1, 2*, Jiale Shao2*, Feng Zhang2, Jian Wang2, Yunhua Xiao1, Zhijun Cheng2#, Wenbang Tang1, 4#, Jianmin Wan2, 3#
1 College of Agronomy, Hunan Agricultural University, Changsha 410128, China
2 National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3 State Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
4 State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
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摘要  小粒水稻不育系卓201S (Z201S) 的开发和应用显示了其在机械化杂交水稻制种方面的潜力,从而显著降低制种成本。然而,调控201S小粒特性的分子机制尚不清楚。本研究利用小粒水稻不育系卓201S和普通粒型水稻品种R2115构建的近等基因系进行了遗传分析。结果表明,Z201S的小粒性状是由一个部分显性基因控制,同时提高了穗粒数。利用图位克隆的方法,将目标基因定位在2号染色体短臂、分子标记LB354和LB63之间约113 kb区间内。转基因分析和基因表达分析显示LOC_Os02g14760是最可能的候选基因,表明Z201S的小粒性状由一个新的基因位点控制。

Abstract  The development and application of the small-grain rice sterile line Zhuo201S (Z201S) has demonstrated its potential for mechanized hybrid rice seed production, leading to significant cost reductions.  However, the molecular mechanism responsible for the small-grain size characteristic of Z201S remains unclear.  In this study, we conducted a genetic analysis using near-isogenic lines constructed from Z210S, a small-grain rice sterile line, and R2115, a normal-grain variety.  The results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain number.  Through mapping, we localized the causal gene to the short arm of chromosome 2, within a 113 kb physical region delimited by the molecular markers S2-4-1 and LB63.  Transgenic analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene, suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.
Keywords:  rice       grain size         map-based cloning  
Received: 05 March 2023   Accepted: 06 July 2023
Fund: This research was supported by the National Natural Science Foundation of China (32172078 and U22A20502).
About author:  #Correspondence Zhijun Cheng, E-mail: chengzhijun@caas.cn; Wenbang Tang, E-mail: tangwenbang@163.com; Jianmin Wan, E-mail: wanjianmin@caas.cn * These authors contributed equally to this study.

Cite this article: 

Bin Lei, Jiale Shao, Feng Zhang, Jian Wang, Yunhua Xiao, Zhijun Cheng, Wenbang Tang, Jianmin Wan. 2024. Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S. Journal of Integrative Agriculture, 23(7): 2155-2163.

Bravo J, Aguilar-Henonin L, Olmedo G. 2005. Four distinct classes of proteins as interaction partners of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. Molecular Genetics and Genomics, 272, 651–665.

Che R H, Tong H N, Shi B H. 2015. Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nature Plants, 2, 15195.

Chen L Y, Lei D Y, Tang W B, Deng H B, Xiao Y H, Zhang G L. 2015. Challenges and strategies of hybrid rice development. Hybrid Rice, 30, 1–4. (in Chinese)

Cheng S H. 2022. Yuan Longping’s strategy on global development of hybrid rice. Hybrid Rice, 37, 123–127. (in Chinese)

Dong N Q, Sun Y W, Guo T. 2020. UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nature Communications, 11, 2629.

Duan P G, Ni S, Wang J M. 2015. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice. Nature Plants, 2, 15203.

Fan C C, Xing Y Z, Mao H L. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 112, 1164–1171.

Hu J, Wang Y X, Fang Y X. 2015. A rare allele of GS2 enhances grain size and grain yield in rice. Molecular Plant 8, 1455–1465.

Hu Z J, He H H, Zhang S Y. 2012. A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice. Journal of Integrative Plant Biology, 54, 979–990.

Hu Z J, Lu S J, Wang M J. 2018. A novel QTL qTGW3 encodes the GSK3/SHAGGY-Like Kinase OsGSK5/OsSK41 that interacts with OsARF4 to negatively regulate grain size and weight in rice. Molecular Plant, 11, 736–749.

Huang K, Wang D K, Duan P G. 2017. WIDE AND THICK GRAIN 1, which encodes an otubain-like protease with deubiquitination activity, influences grain size and shape in rice. Plant Journal, 91, 849–860.

Huang R Y, Jiang L R, Zheng J S. 2013. Genetic bases of rice grain shape: So many genes, so little known. Trends in Plant Science, 18, 218–226.

Ishimaru K, Hirotsu N, Madoka Y. 2013. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nature Genetics, 45, 707–711.

Jiang H Z, Zhang A P, Liu X T. 2022. Grain size associated genes and the molecular regulatory mechanism in rice. International Journal of Molecular Sciences, 23, 3169.

Kariola T, Brader G, Helenius E. 2006. EARLY RESPONSIVE TO DEHYDRATION 15, a negative regulator of abscisic acid responses in Arabidopsis. Plant Physiology, 142, 1559–1573.

Khan R M, Yu P, Sun L. 2021. DCET1 controls male sterility through callose regulation, exine formation, and tapetal programmed cell death in rice. Frontiers in Genetics, 12, 790789.

Kiyosue T, Yamaguchi-Shinozaki K, Shinozaki K. 1994. Cloning of cDNAs for genes that are early-responsive to dehydration stress (ERDs) in Arabidopsis thaliana L.: Identification of three ERDs as HSP cognate genes. Plant Molecular Biology, 25, 791–798.

Li Y B, Fan C C, Xing Y Z. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 43, 1266–1269.

Liu J F, Chen J, Zheng X M. 2017. GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nature Plants, 3, 17043.

Liu Q, Han R X, Wu K. 2018. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nature Communications, 9, 852.

López-Juárez Z M, Aguilar-Henonin L, Guzmán P. 2021. The ATXN2 orthologs CID3 and CID4, act redundantly to in-fluence developmental pathways throughout the life cycle of Arabidopsis thaliana. International Journal of Molecular Sciences, 22, 3068.

Maruyama k, Kato H, Araki H. 1991. Mechanized production of F1 seeds in rice by mixed planting. Japan Agricultural Research Quarterly, 24, 243–252.

Qi P, Lin Y S, Song X J. 2012. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Research, 22, 1666–1680.

Qiao J Y, Jiang H Z, Lin Y Q. 2021. A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice. Molecular Plant, 14, 1683–1698.

Reichel M, Liao Y L, Rettel M. 2016. In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings. Plant Cell, 28, 2435–2452.

Ruan B P, Shang L G, Zhang B. 2020. Natural variation in the promoter of TGW2 determines grain width and weight in rice. New Phytologist, 227, 629–640.

Shi C L, Dong N Q, Guo T. 2020. A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway. Plant Journal, 103, 1174–1188.

Shi C L, Ren Y L, Liu L L. 2019. Ubiquitin specific protease 15 has an important role in regulating grain width and size in rice. Plant Physiology, 180, 381–391.

Si L Z, Chen J Y, Huang X H. 2016. OsSPL13 controls grain size in cultivated rice. Nature Genetics, 48, 447–456.

Song X J, Huang W, Shi M. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics, 39, 623–630.

Song X J, Kuroha T, Ayano M. 2015. Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proceedings of the National Academy of Sciences of the United States of America, 112, 76–81.

Sweeney M, Mccouch S. 2007. The complex history of the domestication of rice. Annals of Botany, 100, 951–957.

Tsumoto Y, Yoshizumi T, Kuroda H. 2006. Light-dependent polyploidy control by a CUE protein variant in Arabidopsis. Plant Molecular Biology, 61, 817–828.

Wang A H, Hou Q Q, Si L Z. 2019. The PLATZ transcription factor GL6 affects grain length and number in rice. Plant Physiology, 180, 2077–2090.

Wang S K, Li S, Liu Q. 2015. The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics, 47, 949–954.

Wang S S, Wu K, Qian Q. 2017. Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Research, 27, 1142–1156.

Wu W G, Liu X Y, Wang M H. 2017. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 3, 17064.

Xu C J, Liu Y, Li Y B. 2015. Differential expression of GS5 regulates grain size in rice. Journal of Experimental Botany, 66, 2611–2623.

Yu J P, Xiong H Y, Zhu X Y. 2017. OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap. BMC Biology, 15, 28.

Zhang Q F. 2007. Strategies for developing Green Super Rice. Proceedings of the National Academy of Sciences of the United States of America, 104, 16402–16409.

Zhang X J, Wang J F, Huang J. 2012. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences of the United States of America, 109, 21534–21539.

Zhao D S, Li Q F, Zhang C Q. 2018. GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nature Communications, 9, 1240.

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