一种水稻微效QTL精细定位和克隆新途径
收稿日期: 2020-12-09
修回日期: 2021-01-24
网络出版日期: 2021-07-10
基金资助
浙江省“万人计划”杰出人才基金资助项目（2020R51007）;中央级公益性科研院所基本科研业务费专项（CPSIBRF-CNRRI-202112）;水稻生物学国家重点实验室课题（2020ZZKT10105）
A New Approach for Fine-mapping and Map-based Cloning of Minor-Effect QTL in Rice
Received date: 2020-12-09
Revised date: 2021-01-24
Online published: 2021-07-10
水稻重要农艺性状一般由少数主效QTL和大量微效QTL共同控制。水稻主效QTL克隆已取得显著进展,而微效QTL由于遗传作用弱,表型鉴定易受测量误差影响,克隆进展缓慢,但微效QTL在水稻重要农艺性状调控中的作用不容忽视。本文介绍了一种水稻微效QTL精细定位和克隆的新途径。该途径包含2个阶段：1）应用剩余杂合体构建近等基因系群体进行目标QTL的精细定位;2）应用基因编辑技术创制候选基因突变体验证基因功能。应用该策略笔者所在团队在水稻第1染色体长臂精细定位了6个微效粒重和粒型QTL,并成功克隆首个微效粒重QTL。该技术可在方法上为水稻QTL克隆及新种质创制提供更多选择。
朱玉君, 左紫薇, 张振华, 樊叶杨 . 一种水稻微效QTL精细定位和克隆新途径[J]. 中国水稻科学, 2021 , 35(4) : 407 -414 . DOI: 10.16819/j.1001-7216.2021.201206
Important agronomic traits in rice are generally controlled by a few major-effect QTLs and a large number of minor-effect QTLs. Great progresses have been made in the cloning of major QTLs, while minor QTLs remain difficult to be cloned due to their small genetic effects and the influence of measurement error. A new approach for fine-mapping and map-based cloning of rice minor-effect QTL was introduced in this article. The approach includes two steps: 1) Use the residual heterozygote to construct near isogenic lines for fine-mapping of the target QTL; 2) Use the genome editing to create mutants of candidate genes for gene function identification. Using the strategy, we fine-mapped six minor QTLs for grain weight and grain size on the long arm of chromosome 1, and successfully cloned the first minor QTL for grain weight. We expect that this approach could provide more options for QTL cloning and new germplasm creation.
Key words： rice (Oryza sativa L.); grain size; minor QTL; map-based cloning
| [1] | Ashikari M, Sakakibara H, Lin S, Yanamoto T, Takashi T, Nishimura A, Angeles R E, Qian Q, Kitano H, Matsuoka M.Cytokinin oxidase regulates rice grain production[J]. Science, 2005, 309: 741-745. |
| [2] | Huo X, Wu S, Zhu Z, Liu F, Fu Y, Cai H, Sun X, Gu P, Xie D, Tan L, Sun C.NOG1 increases grain production in rice[J]. Nature Communications, 2017, 8: 1497. |
| [3] | Zhang Z, Wang K, Guo L, Zhu Y, Fan Y, Cheng S, Zhuang J.Pleiotropism of the photoperiod-insensitive allele of Hd1 on heading date, plant height and yield traits in rice[J]. PLoS ONE, 2012, 7: e52538. |
| [4] | Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q.Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice[J]. Nature Genetics, 2008, 40: 761-767. |
| [5] | Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J.DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously[J]. Plant Physiology, 2010, 153: 1747-1758. |
| [6] | Yan W H, Wang P, Chen H X, Zhou H J, Li Q P, Wang C R, Ding Z H, Zhang Y S, Yu S B, Xing Y Z, Zhang Q F.A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice[J]. Molecular Plant, 2011, 4: 319-330. |
| [7] | Zhang Z H, Cao L Y, Chen J Y, Zhang Y X, Zhuang J Y, Cheng S H.Effects of Hd2 in the presence of the photoperiod-insensitive functional allele of Hd1 in rice[J]. Biology Open, 2016, 5: 1719-1726. |
| [8] | Zhu Y, Fan Y, Wang K, Huang D, Liu W, Ying J, Zhuang J.Rice flowering locus T 1 plays an important role in heading date influencing yield traits in rice[J]. Scientific Reports, 2017, 7: 4918. |
| [9] | Li N, Xu R, Li Y.Molecular networks of seed size control in plants[J]. Annual Reviews of Plant Biology, 2019, 70: 11. |
| [10] | Wang A, Hou Q, Si L, Huang X, Luo J, Lu D, Zhu J, Shangguan Y, Miao J, Xie Y, Wang Y, Zhao Q, Feng Q, Zhou C, Li Y, Fan D, Lu Y, Tian Q, Wang Z, Han B.The PLATZ transcription factor GL6 affect grain length and number in rice[J]. Plant Physiol, 2019, 180: 2077-2090. |
| [11] | Ruan B, Shang L, Zhang B, Hu J, Wang Y, Lin H, Zhang A, Liu C, Peng Y, Zhu L, Ren D, Shen L, Dong G, Zhang G, Zeng D, Guo L, Qian Q, Gao Z.Natural variation in the promoter of TGW2 determines grain width and weight in rice[J]. New Phytologist, 2020, 227(2): 3. |
| [12] | Shi C L, Dong N Q, Guo T, Ye W W, Shan J X, Lin H X.A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway[J]. Plant Journal, 2020, doi: 10.1111/tpj.14793. |
| [13] | Li Q, Lu L, Liu H, Bai X, Zhou X, Wu B, Yuan M, Yang L, Xing Y.A minor QTL, SG3, encoding an R2R3-MYB protein, negatively controls grain length in rice[J]. Theoretical and Applied Genetics, 2020, 133: 2387-2399. doi.org/10.1007/s00122-020-03606-z. |
| [14] | Dong N Q, Sun Y, Guo T, Shi C L, Zhang Y M, Kan Y, Xiang Y H, Zhang H, Yang Y B, Li Y C, Zhao H Y, Yu H X, Lu Z Q, Wang Y, Ye W W, Shan J X, Lin H X.UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice[J]. Nature Communications, 2020, doi.org/10.1038/s41467-020-16403-5. |
| [15] | Chan A N, Wang L L, Zhu Y J, Fan Y Y, Zhuang J Y, Zhuang Z H. Identification through fine mapping and verification using CRISRP/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice[J]. Theoretical and Applied Genetics, 2021, 134: 327-337. https://doi.org/10.1007/s00122-020-03699-6. |
| [16] | Noriko K, Masayuki K, Kei K, Takuya K, Tsutomu N, Yuji H, Itsuro T, Takashi S, Kiyoaki K.Identification of quantitative trait loci for rice grain quality and yield-related traits in two closely related Oryza L. subsp. japonica cultivars grown near the northernmost limit for rice paddy cultivation[J]. Breeding Science, 2017, 67: 191-206. |
| [17] | Zhang H W, Fan Y Y, Zhu Y J, Chen J Y, Yu S B, Zhuang J Y.Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice[J]. BMC Genetics, 2016, 17: 98-107. |
| [18] | Wang L L, Chen Y Y, Guo L, Zhang H W, Fan Y Y, Zhuang J Y.Dissection of qTGW1.2 to three QTLs for grain weight and grain size in rice (Oryza sativa L.)[J]. Euphytica, 2015, 202: 119-127. |
| [19] | Dong Q, Zhang Z H, Wang LL, Zhu Y J, Fan Y Y, Mou T M, Ma L Y, Zhuang J Y.Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice[J]. Rice, 2018, 11: 44. |
| [20] | Wang W, Wang L, Zhu Y, Fan Y, Zhuang J.Fine-mapping of qTGW1.2a, a quantitative trait locus for 1000-grain weight in rice[J]. Rice Science, 2019, 26(4): 220-228. |
| [21] | Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna J A, Charpentier E.A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337: 816. |
| [22] | Hu X, Meng X, Liu Q, Wang K.Increasing the efficiency of CRISPR-Cas9-VQR precise genome editing in rice[J]. Plant Biotechnology Journal, 2018, 16: 292-297. |
| [23] | Meng X, Hu X, Liu Q, Song X, Gao C, Li J, Wang K.Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice[J]. Science China: Life Science, 2018, 61: 122-125. |
| [24] | Shan Q, Wang Y, Li J, Gao C.Genome editing in rice and wheat using the CRISPR/Cas system[J]. Nature Protocol, 2014, 9: 2395-2410. |
| [25] | Zhao D S, Li Q F, Zhang C Q, Zhang C, Yang Q Q, Pan L X, Ren X Y, Lu J, Gu M H, Liu Q Q.GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality[J]. Nature Communications, 2018, 9: 1240. |
| [26] | Ying J Z, Ma M, Bai C, Huang X H, Liu J L, Fan Y Y, Song X J.TGW3, a major QTL that negatively modulates grain length and weight in rice[J]. Molecular Plant, 2018, 11: 750-753. |
| [27] | Zhuang J Y, Fan Y Y, Rao Z M, Wu J L, Xia Y W, Zheng K L.Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice[J]. Theoretical and Applied Genetics, 2002, 105: 1137-1145. |
| [28] | Guo L, Wang K, Chen J, Huang D, Fan Y, Zhuang J Y.Dissection of two quantitative trait loci for grain weight linked in repulsion on the long arm of chromosome 1 of rice (Oryza sativa L.)[J]. Crop Journal, 2013, 1: 70-76. |
| [29] | Li N, Xu R, Duan P, Li Y H.Control of grain size in rice.Plant Reproduction, 2018, 31: 237-251. DOI: 10.1007/ s00497-018-0333-6. |
| [30] | 刘喜, 牟昌铃, 周春雷, 程治军, 江玲, 万建民. 水稻粒型基因克隆和调控机制研究进展[J]. 中国水稻科学, 2018, 32(1): 1-11. |
| [30] | Liu X, Mou C, Zhou C, Cheng Z, Jiang L, Wang J.Research progress on cloning and regulation mechanism of rice grain shapes genes[J]. Chinese Journal of Rice Science, 2018, 32(1): 1-11. (in Chinese with English abstract). |
| [31] | Fan Y, Li Y.Molecular, cellular and Yin-Yang regulation of grain size and number in rice[J]. Molecular Breeding, 2019, 39: 163. |
| [32] | 康艺维, 陈玉宇, 张迎信. 水稻粒型基因克隆研究进展及育种应用展望[J]. 中国水稻科学, 2020, 34(6): 479-490. |
| [32] | Kang Y W, Chen Y Y, Zhang Y X.Research progress and breeding prospects of grain size associated genes in rice[J]. Chinese Journal of Rice Science, 2020, 34(6): 479-490. (in Chinese with English abstract). |
| [33] | Song X J, Huang W, Shi M, Zhu M Z, Lin H X.A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase[J]. Nature Genetics, 2007, 39: 623-630. |
| [34] | Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H, Shi Z, Pan J, Zhang D, Kang S, Zhu L, Dong G, Guo L, Zeng D, Zhang G, Xie L, Xiong G, Li J, Qian Q.A rare allele of GS2 enhances grain size and grain yield in rice[J]. Molecular Plant, 2015, 8: 1455-1465. |
| [35] | Duan P, Ni S, Wang J, Zhang B, Xu R, Wang Y, Chen H, Zhu X, Li Y.Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice[J]. Nature Plants, 2016, 2: 15203. |
| [36] | Che R, Tong H, Shi B, Liu Y, Fang S, Liu D, Xiao Y, Hu B, Liu L, Wang H, Zhao M, Chu C.Control of grain size and rice yield by GL2-mediated brassinosteroid responses[J]. Nature Plants, 2016, 2. |
| [37] | Yu J, Xiong H, Zhu X, Zhang H, Li H, Miao J, Wang W, Tang Z, Zhang Z, Yao G, Zhang Q, Pan Y, Wang X, Rashid MAR, Li J, Gao Y, Li Z, Yang W, Fu X, Li Z,.OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap[J]. BMC Biology, 2017, 15: 28-45. |
| [38] | Yu J, Miao J, Zhang Z, Xiong H, Zhu X, Sun X, Pan Y, Liang Y, Zhang Q, Rashid MAR, Li J, Zhang H, Li Z.Alternative splicing of OsLG3b controls grain length and yield in japonica rice[J]. Plant Biotechnology Journal, 2018, doi:10.1111/pbi.12903. |
| [39] | Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S, Chen J, Pan Y, Li Q, Xu X, Zhou J, Tao D, Wu Y, Fu X.G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice[J]. Nature Communications, 2018, 9: 852. |
| [40] | Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q.GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein[J]. Theoretical and Applied Genetics, 2006, 112: 1164-1171. |
| [41] | Qi P, Lin Y S, Song X J, Shen J B, Huang W, Shan J X, Zhu M Z, Jiang L, Gao J P, Lin H X.The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3[J]. Cell Research, 2012, 22: 1666-1680. |
| [42] | Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J, Zhang H. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice [J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 26, 109: 21 534-21 539. |
| [43] | Hu Z, Lu S J, Wang M J, He H, Sun L, Wang H, Liu X H, Jiang L, Sun J L, Xin X, Kong W, Chu C, Xue H W, Yang J, Luo X, Liu J X.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[J]. Molecular Plant, 2018, 11: 736-749. |
| [44] | Xia D, Zhou H, Liu R, Dan W, Li P, Wu B, Chen J, Wang L, Gao G, Zhang Q, He Y.GL3.3, a novel QTL encoding a GSK3/SHAGGY-like kinase, epistatically interacts with GS3 to form extra-long grains in rice[J]. Molecular Plant, 2018, 11: 754-756. |
| [45] | Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q.Natural variation in GS5 plays an important role in regulating grain size and yield in rice[J]. Nature Genetics, 2011, 43: 1266-1269. |
| [46] | Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M.Deletion in a gene associated with grain size increased yields during rice domestication[J]. Nature Genetics, 2008, 40(8): 1023-1028. |
| [47] | Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J.Isolation and initial characterization of GW5, a major QTL associated with grain width and weight[J]. Cell Research, 2008, 18: 1199-1209. |
| [48] | Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu Bun-ichi, Onishi A, Miyagawa H, Katoh E.Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield[J]. Nature Genetics, 2013, 45: 707-711. |
| [49] | Song X J, Kuroha T, Ayano M, Furuta T, Nagai K, Komeda N, Segami S, Miura K, Ogawa D, Kamura T, Suzuki T, Higashiyama T, Yamasaki M, Mori H, Inukai Y, Wu J, Kitano H, Sakakibara H, Jacobsen S E, Ashikari M.Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice[J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112: 76-81. |
| [50] | Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, Weng Q, Wang Y, Zhan Q, Liu K, Wei X, An K, An G, Han B.OsSPL13 controls grain size in cultivated rice[J]. Nature Genetics, 2016, 48: 447-456. |
| [51] | Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W, Meng X, Liu R, Chen H, Jing Y, Wang Y, Zhu X, Li J, Qian Q.Copy number variation at the GL7 locus contributes to grain size diversity in rice[J]. Nature Genetics, 2015, 47: 944-948. |
| [52] | Wang S, Li S, Liu Q, Wu K, Zhang J, Wang S, Wang Y, Chen X, Zhang Y, Gao C, Wang F, Huang H, Fu X.The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality[J]. Nature Genetics, 2015, 47: 949-954. |
| [53] | Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X.Control of grain size, shape and quality by OsSPL16 in rice[J]. Nature Genetics, 2012, 44: 950-954. |
| [54] | Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler S E, Qian Q, Zhang Q-F, Li J, Han B.Genome-wide association studies of 14 agronomic traits in rice landraces[J]. Nature Genetics, 2010, 42(11): 961-969. |
| [55] | Huang L, Zhang R, Huang G, Li Y, Melaku G, Zhang S, Chen H, Zhao Y, Zhang J, Zhang Y, Hu F.Developing superior alleles of yield genes in rice by artificial mutagenesis using the CRISPR/Cas9 system[J]. Crop Journal, 2018, 6: 475-481. |
| [56] | Wang C, Liu Q, Shen Y, Hua Y, Wang J, Lin J, Wu M, Sun T, Cheng Z, Mercier R, Wang K.Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes[J]. Nature Biotechnology, 2019, doi.org/10.1038/s41587-018-0003-0. |
| [57] | Li S, Shen L, Hu P, Liu Q, Zhu X, Qian Q, Wang K, Wang Y.Developing disease-resistant thermosensitive male sterile rice by multiplex gene editing[J]. Journal of Integrative Plant Biology, 2019, doi: 10.1111/jipb.12774. |
| [58] | 黄忠明, 周延彪, 唐晓丹, 赵新辉, 周在为, 符星学, 王凯, 史江伟, 李艳锋, 符辰建, 杨远柱. 基于CRISPR/Cas9技术的水稻温敏不育基因tms5突变体的构建[J]. 作物学报, 2018, 44(6): 844-851. |
| [58] | Huang Z M, Zhou Y B, Tang X D, Zhao X H, Zhou Z W, Fu X X, Wang K, Shi J W, Li Y F, Fu C J, Yang Y Z.Construction of tms5 mutants in rice based on CRISPR/Cas9 technology[J]. Acta Agronomica Sinica, 2018, 44(6): 844-851. (in Chinese with English abstract). |
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