Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (02): 240-252.doi: 10.3724/SP.J.1006.2014.00240

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Identification of Expressed Resistance Gene Analogues (RGAs) and Development of RGA-SSR Markers in Nicotiana

YUAN Qing-Hua,XIE Rui-Hong,ZHANG Zhen-Chen,MA Zhu-Wen,LI Ji-Qin,LI Shu-Ling,CHEN Jun-Biao*   

  1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
  • Received:2013-06-02 Revised:2013-07-25 Online:2014-02-12 Published:2013-10-22

Abstract:

Tobacco is an important cash crop and an ideal experimental system for studies on plant-pathogen interaction. Identification of tobacco R gene and resistance gene analogs is propitious to elucidating the underlying resistant mechanisms. In recent years, the growing public tobacco EST data provide rich source for identifying expressed RGA. In this study, 149 606 Uni-EST were assembled from 412 325 ESTs of tobacco in GenBank. By scanning the Uni-EST with 112 plant R gene protein sequences 1113 NtRGAs were identified. These expressed RGAs comprised 273, 546, 53, 102, and 30 of NBS-LRR, LRR-PK, LRR, PK, and Mlo domains encoding R genes, respectively. No domain was detected in the rest of 109 RGAs. By aligning sequence 1079 NtRGAs were allocated on 712 loci in N. benthamiana A total of 78 simple sequence repeats (SSRs) were identified from 72NtRGAs. Sixty-four primer pairs were designed base on the flanking sequence of SSR. Among them, 54 primer pairs were amplified with clear bands from tobacco genomic DNA. Nine primer pairs were detected to have polymorphism among 24 varieties of Nicotiana tabacum with two to four alleles (on average 2.56 alleles). Forty-one primer pairs were detected to have polymorphism among six species in Nicotiana with two to four alleles (on average 2.61 alleles).genome.

Key words: Nicotiana, Expressed sequence tags, Resistance gene analogs, SSR

[1]Ellis J, Dodds P, Pryor T. The generation of plant disease resistance gene specificities. Trends Plant Sci, 2000, 5: 373–379



[2]Sanseverino W, Roma G, Simone M D, Faino L, Melito S, Stupka E, Frusciante L, Ercolano M R. PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucl Acids Res, 2009, 38: D815



[3]Johal G S, Briggs S P. Reductase activity encoded by the Hm1 disease resistance gene in maize. Science, 1992, 258: 985–987



[4]Whitham S, McCormick S, Baker B. The N gene of tobacco confers resistance to tobacco mosaic virus in transgenic tomato. Proc Natl Acad Sci USA, 1996, 93: 8776–8781



[5]Dixon M S, Jones D A, Keddie J S, Thomas C M, Harrison K, Jones J D G, Lane C. The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat protein. Cell, 1996, 84: 451–459



[6]Bent A F. Plant disease resistance genes: function meets structure. Plant Cell, 1996, 8: 1757–1771



[7]Meyers B C, Dickerman A W, Michelmore R W, Sivaramakrishnan S, Sobral B W, Young N D. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J, 1999, 20: 317–332



[8]Hulbert S H, Webb C A, Smith S M, Sun Q. Resistance gene complexes: evolution and utilization. Annu Rev Phytopathol, 2001, 39: 285–312



[9]Dangl J L, Jones J D: Plant pathogens and integrated defence responses to infection. Nature, 2001, 411: 826–833



[10]Meyers B C, Kozik A, Griego A, Kuang H, Michelmore R W. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 2003, 15: 809–834



[11]Bent A F, Kunkel B N, Dahlbeck D, Brown K L, Schmidt R, Giraudat J, Leung J, Staskawicz B J: RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science, 1994, 265: 1856–1860



[12]Dunning F M, Sun W, Jansen K L, Helft L, Bent A F. Identification and mutational analysis of Arabidopsis FLS2 leucine-rich repeat domain residues that contribute to flagellin perception. Plant Cell, 2007, 19: 3297–3313



[13]Song W Y, Wang G L, Chen L L, Kim H S, Pi L Y, Holsten T, Gardner J, Wang B, Zhai W X, Zhu L H, Fauquet C, Ronald P. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science, 1995, 270: 1804–1806



[14]Tor M, Brown D, Cooper A, Woods-Tor A, Sjolander K, Jones J D, Holub E B. Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9. Plant Physiol, 2004, 135: 1100–1112



[15]Martin G B, Brommonschenkel S H, Chunwongse J, Frary A, Ganal M W, Spivey R, Wu T, Earle E D, Tanksley S D. Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science, 1993, 262: 1432–1436



[16]Taler D, Galperin M, Benjamin I, CohenY, Kenigsbuch D. Plant eR genes that encode photorespiratory enzymes confer resistance against disease. Plant Cell, 2004, 16: 172–184



[17]Buschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, DieRGLarde P, Groenendijk J, Topsch S, Vos P, Salamini F, Schulze-Lefert P. The barley Mlo gene: a novel control element of plant pathogen resistance. Cell, 1997, 88: 695–705



[18]Botella M A, Coleman M J, Hughes D E, Nishimura M T, Jones J D G, Somerville S C. Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes. Plant J, 1997, 12: 1197–1211



[19]Aarts M G M, Hekkert B L, Holub E B, Beynon J L, Stiekema W J, Pereira A. Identification of R-gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana. Mol Plant Microbe Interact, 1998, 11: 251–258



[20]Graham M A, Marek L F, Lohnes D, Cregan P, Shoemaker R C. Expression and genome oRGLnization of resistance gene analogs in soybean. Genome, 2000, 43: 86–93



[21]Mago R, Nair S, Mohan M. Resistance gene analogues from rice: cloning, sequencing and mapping. Theor Appl Genet, 1999, 99: 50–57



[22]Collins N C, Webb C A, Seah S, Ellis J G, Hulbert S H, Pryor A. The isolation and mapping of disease resistance gene analogs in maize. Mol Plant Microbe Interact, 1998, 11: 968–978



[23]Seah S, Sivasithamparam K, Karakousis A, Lagudah E S. Cloning and characterization of a family of disease resistance gene analogs from wheat and barley. Theor Appl Genet, 1998, 97: 937–945



[24]Leng X, Xiao B, Wang S, Gui Y, Wang Y, Lu X, Xie J, Li Y, Fan L. Identification of NBS-type resistance gene homologs in tobacco genome. Plant Mol Biol Rep, 2010, 28: 152–161



[25]Gao Y L, Xu Z L, Jiao F C, Yu H Q, Xiao B G, Li Y P, Lu X P. Cloning, structural features, and expression analysis of resistance gene analogs in tobacco. Mol Biol Rep, 2010, 37: 345–354



[26]Wan H J, Zhao Z G, Malik A, Qian C T, Chen J F. Identification and characterization of potential NBS-encoding resistance genes and induction kinetics of a putative candidate gene associated with downy mildew resistance in Cucumis. BMC plant Biol, 2010, 10: 186



[27]Huettel B, Santra D, Muehlbauer J, Kahl G. Resistance gene analogues of chickpea (Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster. Theor Appl Genet, 2002, 105: 479–490



[28]Nair R A, Thomas G. Isolation, characterization and expression studies of resistance gene candidates (RGCs) from Zingiber spp. Theor Appl Genet, 2007, 116: 123–134



[29]Bertioli D J, Leal-Bertioli S C, Lion M B, Santos V L, Pappas G, Cannon S B, Guimaraes P M. A large scale analysis of resistance gene homologues in Arachis. Mol Gen Genomics, 2003, 270: 35–45



[30]Monsi B, Wisser R J, Pennill L, Hulbert S H. Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet, 2004, 109: 1434–1447



[31]Ameline-Torregrosa C, Wang B B, O'Bleness M S, Deshpande S, Zhu H Y, Roe B, Young N D, Cannon S B. Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol, 2008, 146: 5–21



[32]Li X Y, Cheng Y, Ma W, Zhao Y, Jiang H Y, Zhang M. Identification and characterization of NBS-encoding disease resistance genes in Lotus japonicus. Plant Syst Evol, 2010, 289: 101–110



[33]Liu Z, Crampton M, Todd A, Kalavacharla V. Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.). BMC Plant Biol, 2012, 12: 42



[34]Liu Z, Feng S, Pandey M K, Chen X, Culbreath A K, Varshney R K, Guo B. Identification of expressed resistance gene analogs from peanut (Arachis hypogaea L.) expressed sequence tags. J Integr Plant Biol, 2013, 55: 453–461



[35]Sanz M J, Loarce Y, Fominaya A, Vossen J H, Ferrer E. Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats. Theor Appl Genet, 2013, 126: 203–218



[36]Loarce Y, Sanz M J, Irigoyen M L, Fominaya A, Ferrer E. Mapping of STS markers obtained from oat resistance gene analog sequences. Genome, 2009, 52: 608–619



[37]Tantasawat P A, Poolsawat O, Prajongjai T, Chaowiset W, Tharapreuksapong A. Association of RGA-SSCP markers with resistance to downy mildew and anthracnose in grapevines. Genet Mol Res, 2012, 11: 1799–1809



[38]Palomino C, Fernández-Romero M D, Rubio J, Torres A, Moreno M T, Millán T. Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance. Theor Appl Genet, 2009, 118: 671–682



[39]Flor H H. The complementary genic systems in flax and flax rust. Adv Genet, 1956, 8: 29–54



[40]Dilbirligi M, Gill K S. Identification and analysis of expressed resistance gene sequences in wheat. Plant Mol Biol, 2003, 53: 771–787



[41]Xiao W K, Xu M L, Zhao J R, Wang F G, Li J S, Dai J R. Genome-wide isolation of resistance gene analogs in maize (Zea mays L.). Theor Appl Genet, 2006, 113: 63–72



[42]Rossi M, Araujo P G, Paulet F, Garsmeur O, Dias V M, Chen H, Van Sluys M A, D’Hont A: Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Genet Genom, 2003, 269: 406–419



[43]Xiao W K, Zhao J, Fan S C, Li L, Dai J R, Xu M L. Mapping of genome-wide resistance gene analogs (RGAs) in maize (Zea mays L.). Theor Appl Genet, 2007, 115: 501–508



[44]He L, Du C, Covaleda L, Xu Z, Robinson A F, Yu J Z, Kohel R J, Zhang H B. Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.). Mol Plant Microbe Interact, 2004, 17: 1234–1241



[45]Peñuela S, Danesh D, Young N D. Targeted isolation, sequence analysis, and physical mapping of nonTIR NBS-LRR genes in soybean. Theor Appl Genet, 2002, 104: 261–272



[46]Bertioli D J, Moretzsohn M C, Madsen L H, Sandal N, Leal-Bertioli S C, Guimaraes P M, Hougaard B K, Fredslund J, Schauser L, Nielsen A M, Sato S, Tabata S, Cannon S B, Stougaard J. An analyses of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics, 2009, 10: 45



[47]Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N, Van der Hoeven R, Ganal M, Donini P. A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theor Appl Genet, 2011, 23: 219–230

[1] Zhang Ying-Xing, Bheel Chander Kumar, Song Yu-Zhen, Wang Yue, Cao Yue, Khound Rituraj, Santra Dipak Kumar, Cao Xiao-Ning, Wang Rui-Yun. Screening and phenotypic characterization of EMS-induced mutants with elite agronomic traits in broomcorn millet [J]. Acta Agronomica Sinica, 2026, 52(5): 1388-1400.
[2] Tian Chun-Yan, Lu Xin, Wu Cai-Wen, Xu Chao-Hua, Liu Jia-Yong, Bian Xin, Tao Lian-An. Genetic diversity analysis and breeding potential evaluation of innovative sugarcane germplasm based on fluorescent SSR [J]. Acta Agronomica Sinica, 2026, 52(4): 1057-1072.
[3] WANG Hao-Chen, WANG Ke-Jing, HAN Juan, LI Xiang-Hua. Spatial genetic structure characteristics of natural populations of Glycine tomentella in two representative habitats in the southeast coast, China: a study of intrapopulation sampling strategy [J]. Acta Agronomica Sinica, 2025, 51(11): 2875-2885.
[4] ZHENG Dong, ZHOU Xian-Li, TENG Chang-Cai, HOU Wan-Wei, ZHANG Hong-Yan, LIU Yu-Jiao. Genetic relationship analysis and fingerprints construction of faba bean varieties in Qinghai province based on SSR markers [J]. Acta Agronomica Sinica, 2025, 51(1): 79-90.
[5] KUANG Bo-Wen, WEI Ni, LIU Jin-Dian, CHEN Mei-Yan, MAO Xing-Jie, DUAN Wei-Xing, YANG Xi-Ping. Development of SSR markers and database based on genomes of sugarcane and its relatives [J]. Acta Agronomica Sinica, 2025, 51(1): 103-116.
[6] DING Yi-Bing, XIN Xu-Xia, FENG Zhi-Zun, GUO Juan, CAO Yue, CHEN Xi-Ming, WANG Xiao-Dan, CAO Xiao-Ning, SANTRA Dipak K, CHEN Ling, QIAO Zhi-Jun, WANG Rui-Yun. Core germplasm identification of proso millet in spring sowing area of Northeast China using fluorescent microsatellite markers [J]. Acta Agronomica Sinica, 2024, 50(7): 1728-1739.
[7] DING Yi-Bing, XIN Xu-Xia, FENG Zhi-Zun, CAO Yue, GUO Juan, Dipak K SANTRA, WANG Rui-Yun, CHEN Xi-Ming. Core germplasm and DNA molecular identity card of proso millet in Northeast Spring sowing region in China [J]. Acta Agronomica Sinica, 2024, 50(5): 1181-1192.
[8] TIAN Chun-Yan, BIAN Xin, LANG Rong-Bin, YU Hua-Xian, TAO Lian-An, AN Ru-Dong, DONG Li-Hua, ZHANG Yu, JING Yan-Fen. Association analysis of three breeding traits with SSR markers and exploration of elite alleles in sugarcane [J]. Acta Agronomica Sinica, 2024, 50(2): 310-324.
[9] CHEN Tian, LI Yu-Ying, RONG Er-Hua, WU Yu-Xiang. Character identification and floral organ transcriptome analysis on artificial allotetraploids of Gossypium hirsutum L. [J]. Acta Agronomica Sinica, 2024, 50(2): 325-339.
[10] CHEN Zhi-Kai, ZHOU Xian-Li, ZHANG Hong-Yan, TENG Chang-Cai, HOU Wan-Wei. SSR association analysis of the protein content of 320 faba bean germplasms [J]. Acta Agronomica Sinica, 2024, 50(11): 2775-2786.
[11] CAO Yue, Zhang Li-Yuan, XIN Xu-Xia, FENG Zhi-Zun, GUO Juan, WANG Xiao-Dan, CAO Xiao-Ning, SANTRA Dipak K, CHEN Ling, QIAO Zhi-Jun, WANG Rui-Yun. Construction of DNA molecular identity card of proso millet in Ningxia based on fluorescent SSR [J]. Acta Agronomica Sinica, 2024, 50(11): 2699-2711.
[12] GUO Juan, XIN Xu-Xia, FENG Zhi-Zun, CAO Yue, WANG Xiao-Dan, CAO Xiao-Ning, SANTRA Dipak K, CHEN Ling, QIAO Zhi-Jun, WANG Rui-Yun. Molecular identification of broomcorn millet germplasm resources in Shaanxi based on SSR [J]. Acta Agronomica Sinica, 2024, 50(10): 2643-2653.
[13] WANG Qian, ZHANG Li-Yuan, XU Yue, LI Hai, LIU Shao-Xiong, XUE Ya-Peng, LU Ping, WANG Rui-Yun, LIU Min-Xuan. High motif EST-SSR markers development and genetic diversity evaluation for 200 core germplasms in proso millet [J]. Acta Agronomica Sinica, 2023, 49(8): 2308-2318.
[14] CHEN Yi-Hang, TANG Chao-Chen, ZHANG Xiong-Jian, YAO Zhu-Fang, JIANG Bing-Zhi, WANG Zhang-Ying. Construction of core collection of sweetpotato based on phenotypic traits and SSR markers [J]. Acta Agronomica Sinica, 2023, 49(5): 1249-1261.
[15] LI Ying, LIU Hai-Cui, SHI Lyu, SHI Xiao-Xu, HAN Xiao, LIU Jian, WEI Ya-Feng. Genetic diversity and population structure analysis of naked barley germplasm resources in Jiangsu province [J]. Acta Agronomica Sinica, 2023, 49(10): 2687-2697.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!