Mining, genetic mapping and expression analysis of EST-derived resistance gene homologs (RGHs) in cotton

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• 作者：Gaofeng Ren (1)
  Ximei Li (1)
  Zhongxu Lin (1)
  
  1. National Key Laboratory of Crop Genetic Improvement ; Huazhong Agricultural University ; Wuhan ; 430070 ; China
  
• 关键词：Cotton ; PR ; RGAs ; Genetic mapping ; Expression analysis
• 刊名：BMC Plant Biology
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：14
• 期：1
• 全文大小：1,732 KB
• 参考文献：1. Zhu, HQ (2007) A summary of researches on main cotton diseases. Cotton Sci 19: pp. 391-398
  2. Munis, MF, Tu, L, Deng, F, Tan, J, Xu, L, Xu, S, Long, L, Zhang, X (2010) A thaumatin-like protein gene involved in cotton fiber secondary cell wall development enhances resistance against Verticillium dahliae and other stresses in transgenic tobacco. Biochem Biophys Res Commun 393: pp. 38-44 CrossRef
  3. Wei, H, Li, W, Sun, X, Zhu, S, Zhu, J (2013) Systematic analysis and comparison of nucleotide-binding site disease resistance genes in a diploid cotton Gossypium raimondii. PLoS One 8: pp. e68435 CrossRef
  4. Ma, ZY, Wang, XF, Zhang, GY, Liu, SQ, Sun, JZ (2000) Genetic studies of vertical wilt resistance among different types of sea island cotton. Acta Agronomica Sinica 26: pp. 315-321
  5. TU, LL, Zhang, XL, Zhu, LF (2003) Origin, diversity and evolution of NBS-type disease-resistance gene analogues in Sea-island cotton (Gossypium barbadense L.).. Acta Genetic Sinica 30: pp. 1071-1077
  6. Wang, FR, Liu, RZ, Wang, LM, Zhang, CY (2007) Molecular markers of verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Cotton Sci 19: pp. 424-430
  7. Niu, C, Lu, YZ, Yuan, YL, Percy, RG, Ulloa, M, Zhang, JF (2011) Mapping resistance gene analogs (RGAs) in cultivated tetraploid cotton using RGA-AFLP analysis. Euphytica 181: pp. 65-76 CrossRef
  8. Qi, JS, Ma, C, Zhao, LZ, Liu, SE (2000) Study on heredity of Verticillium wilt resistance of G. barbadense L. Cotton Sci 12: pp. 169-171
  9. Gao, YQ, Nie, YC, Zhang, XL (2003) QTL mapping of genes resistant to Verticillium wilt in cotton. Cotton Sci 15: pp. 73-78
  10. Wang, HM, Zhang, XL, He, DH, Lin, ZX, Nie, YC, Li, YH, Chen, W (2005) Detection of DNA markers associated with resistance to Verticillium dahliae in cotton. Acta Phytopathologica Sinica 35: pp. 333-339
  11. Zhang, BC (2006) QTL analysis of fiber quality and resistance to verticillium wilt using Gossypium hirsutum 脳 Gossypium barbadense backcross populations. Master thesis Chin Acad Agr Sci 釁? pp. 釁
  12. Zhen, R, Wang, XF, Ma, ZY (2006) A SSR marker linked with the gene of verticillium wilt resistance in Gossypium barbadense. Cotton Sci 18: pp. 269-272
  13. Yang, C, Guo, WZ, Zhang, TZ (2007) QTL mapping for resistance to verticillium wilt, fiber quality and yield traits in upland cotton (Gossypium hirsutum L.). Mol Plant Breed 5: pp. 797-805
  14. Ge, HY, Wang, YC, GUO, WZ, Zhang, TZ (2008) Inheritance and molecular tagging of resistance against verticillium wilt in upland cotton. Cotton Sci 20: pp. 19-22
  15. Yang, C, Guo, W, Li, G, Gao, F, Lin, S, Zhang, T (2008) QTLs mapping for Verticillium wilt resistance at seedling and maturity stages in Gossypium barbadense L. Plant Sci 174: pp. 290-298 CrossRef
  16. Lanaud, C, Risterucci, AM, Pieretti, I, N鈥橤oran, JAK, Fargeas, D (2004) Characterisation and genetic mapping of resistance and defence gene analogs in cocoa (Theobroma cacao L.). Mol Breed 13: pp. 211-227 CrossRef
  17. Liu, J, Liu, X, Dai, L, Wang, G (2007) Recent progress in elucidating the structure, function and evolution of disease resistance genes in plants. J Genet Genomics 34: pp. 765-776 CrossRef
  18. Monosi, B, Wisser, RJ, Pennill, L, Hulbert, SH (2004) Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet 109: pp. 1434-1447 CrossRef
  19. Donald, TM, Pellerone, F, Adam-Blondon, AF, Bouquet, A, Thomas, MR, Dry, IB (2002) Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine. Theor Appl Genet 104: pp. 610-618 CrossRef
  20. Yan, G, Chen, X, Line, R, Wellings, C (2003) Resistance gene-analog polymorphism markers co-segregating with the Yr5 gene for resistance to wheat stripe rust. Theor Appl Genet 106: pp. 636-643
  21. Gao, YL, Guo, WZ, Wang, L, Zhang, TZ (2006) Isolation and characterization of resistance and defense gene analogs in cotton (Gossypium barbadense L.). Sci China C Life Sci 49: pp. 530-542 CrossRef
  22. He, L, Du, C, Covaleda, L, Xu, Z, Robinson, AF, Yu, JZ, Kohel, RJ, Zhang, HB (2004) Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.). Mol Plant Microbe Interact 17: pp. 1234-1241
  23. Hinchliffe, DJ, Lu, YZ, Potenza, C, Segupta-Gopalan, C, Cantrell, RG, Zhang, JF (2005) Resistance gene analogue markers are mapped to homeologous chromosomes in cultivated tetraploid cotton. Theor Appl Genet 110: pp. 1074-1085 CrossRef
  24. Yu, Y, Yuan, DJ, Liang, SG, Li, XM, Wang, XQ, Lin, ZX, Zhang, XL (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12: pp. 15 CrossRef
  25. Zhu, L, Tu, L, Zeng, F, Liu, D, Zhang, X (2005) An improved simple protocol for isolation of high quality RNA from Gossypium spp. suitable for cDNA library construction. Acta Agron Sin 31: pp. 1657-1659
  釁?
  26. Childs, KL, Hamilton, JP, Zhu, W, Ly, E, Cheung, F, Wu, H, Rabinowicz, PD, Town, CD, Buell, CR, Chan, AP (2007) The TIGR plant transcript assemblies database. Nucleic Acids Res 35: pp. 846-851 CrossRef
  Primer-BLAST: Finding primers specific to your PCR Template.
  Functional and Comparative Genomics of Disease Resistance Gene Homologs.
  27. Marchler-Bauer, A, Anderson, JB, Cherukuri, PF, DeWeese-Scott, C, Geer, LY, Gwadz, M, He, S, Hurwitz, DI, Jackson, JD, Ke, Z (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 33: pp. 192-196 CrossRef
  28. Rajesh, PN, Tekeoglu, M, Gupta, VS, Ranjekar, PK, Muehlbauer, FJ (2002) Molecular mapping and characterization of an RGA locus RGAPtokin1-2171 in chickpea. Euphytica 128: pp. 427-433 CrossRef
  29. Li, XM, Yuan, DJ, Wang, HT, Chen, XM, Wang, B, Lin, ZX, Zhang, XZ (2012) Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 556: pp. 459-470 CrossRef
  30. Stam, P (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 3: pp. 739-744 CrossRef
  31. Kosambi, D (1943) The estimation of map distances from recombination values. Ann Eugen 12: pp. 172-175 CrossRef
  32. Voorrips, RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: pp. 77-78 CrossRef
  33. Devoto, A, Piffanelli, P, Nilsson, I, Wallin, E, Panstruga, R, von Heijne, G, Schulze-Lefert, P (1999) Topology, subcellular localization, and sequence diversity of the Mlo family in plants. J Biol Chem 274: pp. 34993-35004 CrossRef
  34. Hunger, S, Di Gaspero, G, M hring, S, Bellin, D, Sch fer-Pregl, R, Borchardt, DC, Durel, CE, Werber, M, Weisshaar, B, Salamini, F (2003) Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.). Genome 46: pp. 70-82 CrossRef
  35. Shirasu, K, Lahaye, T, Tan, MW, Zhou, F, Azevedo, C, Schulze-Lefert, P (1999) A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell 99: pp. 355-366 CrossRef
  36. Li, F, Fan, G, Wang, K, Sun, F, Yuan, Y, Song, G, Li, Q, Ma, Z, Lu, C, Zou, C, Chen, W, Liang, X, Shang, H, Liu, W, Shi, C, Xiao, G, Gou, C, Ye, W, Xu, X, Zhang, X, Wei, H, Li, Z, Zhang, G, Wang, J, Liu, K, Kohel, RJ, Percy, RG, Yu, JZ, Zhu, Y, Wang, J, Yu, S (2014) Genome sequence of the cultivated cotton Gossypium arboretum. Nat Genet 46: pp. 567-572 CrossRef
  37. Meyers, BC, Kozik, A, Griego, A, Kuang, H, Michelmore, RW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: pp. 809-834 CrossRef
  38. Rossi, M, Araujo, PG, Paulet, F, Garsmeur, O, Dias, VM, Chen, H, Van Sluys, MA, D鈥橦ont, A (2003) Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Genet Genomics 269: pp. 406-419
  
• 刊物主题：Plant Sciences; Agriculture; Tree Biology;
• 出版者：BioMed Central
• ISSN：1471-2229

文摘

Background Cotton is the dominant textile crop and also serves as an important oil crop. An estimated 15% economic loss associated with cotton production in China has been caused by diseases, and no resistance genes have been cloned in this crop. Molecular markers developed from resistance gene homologues (RGHs) might be tightly linked with target genes and could be used for marker-assisted selection (MAS) or gene cloning. Results To genetically map expressed RGHs, 100 potential pathogenesis-related proteins (PRPs) and 215 resistance gene analogs (RGAs) were identified in the cotton expressed sequence tag database, and 347 specific primers were developed. Meanwhile, 61 cotton genome-derived RGA markers and 24 resistance gene analog polymorphism (RGAP) markers from published papers were included to view their genomic distribution. As a result, 38 EST-derived and 17 genome-derived RGH markers were added to our interspecific genetic map. These 55 markers were distributed on 18 of the 26 cotton chromosomes, with 34 markers on 6 chromosomes (Chr03, Chr04, Chr11, Chr17, Chr19 and Chr26). Homologous RGHs tended to be clustered; RGH clusters appeared on 9 chromosomes, with larger clusters on Chr03, Chr04 and Chr19, which suggests that RGH clusters are widely distributed in the cotton genome. Expression analysis showed that 19 RGHs were significantly altered after inoculation with the V991 stain of Verticillium dahliae. Comparative mapping showed that four RGH markers were linked with mapped loci for Verticillium wilt resistance. Conclusions The genetic mapping of RGHs confirmed their clustering in cotton genome. Expression analysis and comparative mapping suggest that EST-derived RGHs participate in cotton resistance. RGH markers are seemed to be useful tools to detected resistance loci and identify candidate resistance genes in cotton.