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中国生物工程杂志

China Biotechnology
China Biotechnology
China Biotechnology  2012, Vol. 32 Issue (03): 115-124    DOI:
    
Research Advance in Map-Based Cloning of Genes in Rice(Oryza sativa L.)
TONG Ji-ping1, LIU Xue-jun1, HAN Ao-nan2, MA Zhong-you1, LIU Min1
1. Tianjin Hybrid Japonica Rice Research Center, Tianjin Crop Institute, Tianjin 300112, China;
2. Forest Technology Department, Anhui Vocational & Technical College of Forestry, Hefei 230031, China
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Abstract  

Map-based cloning refers to a technique for the isolation of genes characterized by a phenotypic alteration usually caused by variation in its DNA sequence. The central procedure used in map-based cloning is the genetic mapping of the gene of interest at extremely high resolution. The high resolution mapping results in the identification of a small interval harboring the gene. Further intermediate steps such as the establishment of clone-based physical maps, the identification of expressed regions and extensive sequencing and sequence annotation may be necessary. Finally, several approaches may be used for the verification of the identified gene harboring a sequence polymorphism. The progress in Map-based cloning of the function genes in rice(Oryza sativa L.) was reviewed.

Key words： Map-based cloning      Segregation population construction      Molecular mapping      Complementation test      Rice(Oryza sativa L.)     
Received: 09 December 2011      Published: 25 March 2012
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TONG Ji-ping, LIU Xue-jun, HAN Ao-nan, MA Zhong-you, LIU Min. Research Advance in Map-Based Cloning of Genes in Rice(Oryza sativa L.). China Biotechnology, 2012, 32(03): 115-124.

URL:

https://manu60.magtech.com.cn/biotech/     OR     https://manu60.magtech.com.cn/biotech/Y2012/V32/I03/115


[1] Coulson A, Sulston J, Brenner S,et al.Toward a physical map of the genome of the nematode Caenorhabditis elegans.Proc. Nati. Acad. Sci. USA,1986,83:7821-7825.

[2] Peters J L, Cnudde F, Gerats T.Forward genetics and map-based cloning approaches. Trends in Plant Science,2003,8(10):484-491.

[3] Tanksley S D,Ganal M W, Martin G B. Chromosome landing:a paradigm for map-based gene cloning in plants with large genomes, Trends Genet, 1995,11(2): 63-68.

[4] Wu K S, Tanksley S D. Abundance polymorphism and genetic mapping of microsatellite in rice. Mol. Gen. Genet. 1993, 241: 225-235.

[5] Lander E S.The new genomics:global views of biology. Science,1996,274:536-539.

[6] Eshed Y,Zamir D.An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield associated QT1.Genetics,1995,141:1147-1162.

[7] Ramsay L D,Jennings D E,Bohuon E J R,et al.The construction of a substitution library of recombinant backcros lines in Brassica oleracea for the precision mapping of quantitative trait loci.Genome,1996,39:558-567.

[8] Tong J P, Liu X J, Zhang Sh Y, et al. Identification, genetic characterization, GA response and molecular mapping of Sdt97, a dominant mutant gene conferring semi-dwarfism in rice (Oryza sativa L.). Genetics Research, 2007,89:221-230.

[9] Nakamura S,Asakawa S,Ohmido N, et al. Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta2 using a highly representative rice BAC library. Mol Gen Genet,1997, 254(6):611-620.

[10] Lovett M, Kere J, Hinton L M. Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proc Natl Acad Sci USA,1991, 88: 9628-9632.

[11] Jander G, Norris S R, Rounsley S D, et al. Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 2002,129: 440-450.

[12] Monna L, Kitazawa N, Yoshino R, et al. Positional cloning of rice semidwarfing gene, sd-1 : rice "Green Revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res, 2002, 9:11-17.

[13] Spielmeyer W, Ellis M H, Chandler P M. Semidwarf ( sd-1 ), 'green revolution'rice, contains a defective gibberellin 20-oxidase gene. PNAS, 2002,99: 9043-9048.

[14] Song W Y,Wang G L,Chen L L, et al. A receptor kinase-like protein encoded by the rice disease resistance gene Xa21.Science, 1995, 270: 1804-1806.

[15] Yano M,Kata Y Y,Ashikari M,et al. Hdl,a major photoperiod sensitivity quantitative trait locus in rice,is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell,2000, 12:2473-2483.

[16] Takahashi Y,Shomura A, Sasaki T, et al. Hd6,a rice quantitative trait locus involved in photoperiod sensitivity,encodes the subunit of protein kinaseCK2.Proc Natl Acad Sci USA,2001,98(14):7922-7927.

[17] Kojima S,Takahashi Y,Kobayashi Y,et al. Hd3a,a rice ortholog of the Arabidopsis FT gene,promotes transition to flowering downstream of Hdl under short-day conditions.Plant cell Physio1,2002,43(10):1096-1105.

[18] Doi K,Izawa T,Fuse T, et al. Ehd1,a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hdl.Genes & Development,2004,l8(8): 926-936.

[19] Xue W Y,Xing Y Z,Weng X Y,et al. Natural variation in Ghd7 is all important regulator of heading date and yield potential in rice,Nature Genetics,2008,40:761-767.

[20] Yan W H,Wang P,Chen H X, et al. A Major QTL,Ghd8,plays pleiotropic roles in regulating grain productivity, plant height,and heading date in rice.Molecular Plant,2011,4(2): 319-330.

[21] Wang E,Wang J J,Zhu X D,et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics,2008,40(11):1370-1374.

[22] Ashikari M,Sakakibara H,Lin S,et al. Cytokinin oxidase regulates rice grain production.Science,2005,309(5735):741-745.

[23] Song X J,Huang W,Shi M,et al. A QTL for rice grain width and weight encodes a reviously unknown RING-type E3 ubiquitin ligase.Nature Genetics,2007,39 (5):623-630.

[24] Fan C C, Xing Y Z, Man H L,et al. GS3,a major QTL for grain length and weight and minor QTL for grain width and thickness in rice,encodes a putative transmembrane protein,Theor.App1.Genet., 2006,l12(6): 1164 -1171.

[25] Weng J F, Gu S H, Wan X Y, et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res, 2008, 18(12): 1199-1209.

[26] Ayahiko S,Takeshi I,Kawom E, et al. Deletion in a gene associated with grain size increased yields during rice domestication,Nature Genetics,2008,40(8):1023-1028.

[27] He G M,Luo X J,Tian F, et al. Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res,2006,16(5):618-626.

[28] 申宗坦,熊振民,朱旭东.2000年稻作展望-中国水稻研究所落成典礼暨稻作科学讨论会论文集.1996,149. Shen Z T, Xiong Z M, Zhu X D.Prospect of Rice for Farming 2000.Hangzhou,Zejiang Science and Technology Press,1996,149.

[29] Ashikari M,Wu J Z,Yano M, et al. Rice gibberellin -insensitive dwarf mutan gene Dwarf1 encodes the a subunit of GTR bindinmg protein, Proc.Natl.Acad. Sci.,1999, 96: 10284 -10289.

[30] Sasaki A, Ashikari M, Ueguchi-Tanaka M, et al. Green revolution: A mutant gibberellin synthesis gene in rice. Nature, 2002,416:701-702.

[31] 许永汉.水稻长节间基因Eui的图位克隆及功能分析.杭州:浙江大学,农业与生物技术学院,2004. Xu Y H.Positional Cloning and Functional Study of Rice Gene Eui Controlling Elongation of Uppermost Internode. Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2004.

[32] 李文强.水稻矮秆基因d62和光叶基因gl1的图位克隆及功能研究.杭州:浙江大学,农业与生物技术学院,2010. Li W Q. Map-based Cloning and Functional Analysis of the Dwarf Gene d62 and Glabrous Gene gl1 in Rice.Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2010.

[33] Li P J,Wang Y H,Qian Q, et al. LAZY1 controls rice shoot gravitropism through regulating polar auxin transport.Cell Research,2007,17(5): 402 -410.

[34] 梁越洋.水稻分蘖基因ext-M1B图位克隆和功能研究.雅安:四川农业大学,农学院, 2010. Liang Y Y.Map-based Cloning and Functional Analysis of Tillering Gene ext-M1B in Rice.Ya'an:Sicuan Agricultural university, College of Agriculture,2010

[35] Li X Y,Qian Q,Fu Z M, et al. Control of tillering in rice. Nature, 2003,422(6932): 618-621.

[36] Jin J,Huang W,Gao J P,et al. Genetic control of rice plant architecture under domestication,Nature Genetics, 2008,40(11):l365-1369.

[37] Tan L B,Li X R,Liu F X,et al. Control of a key transition from prostrate to erect growth in rice domestication.Nature Genetics,2008,40 (11):1360-1364.

[38] Yu B S,Lin Z W,Li H X, et al. TAC1,a major quantitative trait locus controlling tiller angle in rice.Plant J, 2007,52(5):891-898.

[39] Huang, X Z, Qian Q, Liu Z, et al. Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genetics,2009,41(4): 494-497.

[40] Zhou Y, Zhu J, Li Zh, et al. Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication.Genetics,2009,183: 315-324.

[41] Jiao Y Q, Wang Y H, Xue D W, et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nature Genetics,42 (6):541-545.

[42] Miura K, Ikeda M, Matsubara A, et al. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nature Genetics,2010,42 (6):545-550.

[43] 马孝霞.水稻根系发育调控基因OsRGA的克隆及功能研究.杭州:浙江大学,农业与生物技术学院,2010. Ma X X.Cloning and Functional Analysis of OsGatA Controlling Root Development in Rice (Oryza sativa).Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2010.

[44] 张欢欢.水稻根系发育调控基因OsGatB的克隆与功能初步分析.杭州:浙江大学,农业与生物技术学院,2011. Zhan H H. Cloning and Functional Analysis of OsGatB Controlling Root Development in Rice (Oryza sativa).Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2011.

[45] 贾利强.水稻侧根发育基因OsSLR1的克隆和功能研究.杭州:浙江大学,农业与生物技术学院,2008. Jia L G.Cloning and Functional Analysis of Rice Lateral Root Development Related Gene OsSLR1. Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2008.

[46] 何芬芳.水稻OsTUA2基因克隆与功能研究.杭州:浙江大学,农业与生物技术学院,2008. He F F.Cloning and Functional Analysis of OsTUA2. Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2008.

[47] 程龙军.水稻Fe(III)吸收功能缺失突变体Osnaat1的生理生化与分子生物学研究.杭州:浙江大学,农业与生物技术学院,2007. Cheng L J.Physiological and Molecular Biological Analysis on Osnaat1, the Lost Function of Fe(III) Uptake Mutant in Rice.Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2007.

[48] 何晓薇.水稻根毛发育相关基因OsEXP17的克隆和功能研究.杭州:浙江大学,生命科学学院,2008. He X W. Cloning and Functional Analysis of Rice Root Hair Development Related Gene OsEXP17.Hangzhou: Zejiang University, College of Life Sciences, 2008.

[49] 张忠臣.水稻侧根发育基因OsCYP2(cyclophilin2)的克隆和功能分析.杭州:浙江大学,农业与生物技术学院,2007. Zhang Z C.Cloning and Functional Analysis of OsCYP2(Cyclophilin2) in Regulation of Lateral Root Development..Hangzhou: Zejiang University, College of Agriculture and Biotechnology, 2007.

[50] 岳润清.水稻OsSPP基因的克隆和功能研究.杭州:浙江大学,生命科学学院,2009. Yue R Q. Cloning and Functional Analysis ofOsSPP.Hangzhou: Zejiang University, College of Life Sciences, 2009.

[51] 李云峰.水稻小穗不确定性基因LHS1-3和雄蕊雌蕊化基因PS的图位克隆与功能分析.重庆:西南大学,农学与生物科技学院,2008. Li Y F. Map-based Cloning and Functional Analyses of LEAFY HULL STERILE 1-3 (LHS1-3) and PISTILLOID-STAMEN (PS) Genes in Rice (Oryza sativa L. ssp. Indica).Chongqing: Southwest University,College of Agriculture, 2008.

[52] 王红梅.水稻颖壳异常发育突变体Oseg1和Oseg2的基因图位克隆及基因功能分析.上海:上海大学,生命科学学院, 2006. Wang H M. Positional Cloning and Functional Analyses of Rice Glume Developmental Related Genes, Oseg1 and Oseg2.Shanghai:Shanghai University, College of Life Sciences,2006.

[53] 罗增科.水稻花发育相关基因EL1的图位克隆与功能分析.重庆:西南大学,农学与生物科技学院, 2009. Luo Z K. Map-based Cloning and Functional Analysis of EL1 Gene in Rice (Oryza sativa L.ssp. Indica).Chongqing: Southwest University College of Agriculture, 2009.

[54] Wu Z M, Zhang X, He B, et al. A chlorophyll-deficient rice mutant with impaired chlorophyllide esterification in chlorophyll biosynthesis. Plant Physiology, 2007,145(1):29-40.

[55] 王平荣.水稻824ys黄绿叶突变基因的图位克隆及功能分析.雅安:四川农业大学,农学院,2010. Wang P R. Map-based Cloning and Functional Analysis of the 824ys Mutant Gene Controlling Yellow-green Leaf in Rice Ya'an:Sicuan Agricultural University, College of Agriculture,2010.

[56] 胡茂龙.水稻光合功能相关性状QTL分析及转绿型白叶突变体基因的图位克隆.南京:南京农业大学,农学院,2006. Hu M L.QTL Analysis for Traits Associated with Photosynthetic Functions and Map-based Cloning of Virescent White Leaf Gene in Rice (Oryza sativa L.).Nanjing: Nanjing Agricultural University, College of Agriculture,2006.

[57] Huang X Y, Chao D Y, Gao J P, et al. A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control.Genes Dev., 2009, 23(15):1805-1817.

[58] Chen G X, Komatsuda T, Ma J F,et al. An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. PNAS, 2011,108(30):12354-12359.

[59] Du B, Zhang W L, Liu B F, et al. Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proceedings of the National Academy of Sciences USA,2009, 106: 22163-22168.

[60] Gu K Y,Yang B,Tian D S,et al. R gene expression induced by a type-III effector triggers disease resistance in rice. Nature, 2005,435: 1122-1125.

[61] Ren Z H,Gao J P,Li L G,et al. A rice quantitative trait locus for salt tolerance encodes a sodium transporter.Nature Genetics,2005,37 (10):1141-1146.

[62] Ueda T,Sato T,Hidema J, et al. qUVR-10,a major quantitative trait locus for ultraviolet-B resistance in rice,encodes cyclobutane pyrimidine dimerphotolyase.Genetics,2005,171(4):1941-1950.

[63] Xu K,Xu X,Fukao T,et al. SublA is an ethylene-response- factor-like gene that confers submergence tolerance to rice.Nature,2006, 442(7103):705-708.

[64] Saito K, Hayano-Saito Y, Kuroki M, et al. Map-based cloning of the rice cold tolerance gene Ctb1. Plant Science,2010, 179:97-102.

[65] Hu B, Zhu C, Li F, et al. LEAF TIP NECROSIS1 plays a pivotal role in the regulation of multiple phosphate starvation responses in rice. Plant Physiol. 2011,156(3):1101-1115.

[66] Li Y H, Qian Q, Zhou Y H, et al. BRITTLE CULM1,which encode a COBRA-like protein, affects the mechanical properties of rice plants. Plant Cell, 2003,9(15):2020-2031.

[67] Chen J, Ding J, Ouyang Y, et al. A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. PNAS, 2008,105(32): 11436-11441.

[68] 高振宇,曾大力,崔霞,等.水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析.中国科学C辑,2003,33(6):481-487. Gao Z Y,Zeng D L,Cui X, et al.Mapping and genetic analysis of quantitative trait loci for related traits of cooked rice. Science in China (Series C) 2003, 33(6):481-487.

[69] Nishimura A,Ashikari M,Lin S,et al. Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems,Proc Nat1 Acad Sci USA, 2005,102(33): 11940-11944.

[70] Pan G, Zhang X, Liu K, et al. Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides. Plant Mol Biol, 2006,61(6):933-943.

[71] Konishi S,Izawa T,Lin S Y, et al. SNP caused loss of seed shattering during rice domestication.Science,2006,312(5778):1392-1306.

[72] Li C B,Zhou A L, Sang T. Rice domestication by reducing shatering. Science,2006,311(5769):1936-1939.

[73] Komori T, Ohta S, Murai N, et al. Map-based cloning of afertility restorer gene Rf-1, in rice (Oryza sativa L.).Plant J,2004,37:315-325.

[74] Li J, Jiang J F, Qian Q, et al. 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.The Plant Cell, 2011, 23: 628-640.

[75] 许永汉,彭建斐,邓敏娟,等.水稻无叶枕基因克隆及应用研究.核农学报,2010,24(3):436-441. Xu Y H,Peng J F,Deng M J, et al.Cloning and application of a rice liguleless gene.Acta Agriculturae Nucleatae Sinica, 2010, 24(3): 436-441.

[76] 沈一,刘玲珑,刘世家,等.水稻黄胚乳突变体JMW的基因定位与克隆.中国科技论文在线,.http://www. paper.edu.cn:1-9. Sheng Y,Liu L L,Liu S J,et al.Gene Mapping and Cloning of a Yellow Endosperm Mutant in Rice (Oryza sativa L.)..http://www. paper.edu.cn:1-9.

[77] Morot-Gaudry J F, Lea P, Briat J F 著(王元英,时焦主译).植物功能基因组学.北京:中国农业科学技术出版社,2009. Morot-Gaudry J F, Lea P, Briat J F.Functional Plant Genomics. Beijing:Chinese Agricultural Science and Technology Press.2009.
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