AFLP-RGA markers in comparison with RGA and AFLP in cultivated tetraploid cotton

Crop Science

Volumn 47, Issue 1, 2007, Pages 180-187

  Zhang, Jinfa ^a   Yuan, Youlu ^b   Niu, Chen ^a   Hinchliffe, Doug J ^c   Lu, Yingzhi ^a   Yu, Shuxun ^b   Percy, Richard G ^d   Ulloa, Mauricio ^e   Cantrell, Roy G ^f  

^a NEW MEXICO STATE UNIVERSITY   (United States)

^b AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

^c SOUTHERN REGIONAL RESEARCH CENTER   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e U S DEPARTMENT OF AGRICULTURE   (United States)

^f Agricultural and Environmental Research Division   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GOSSYPIUM; GOSSYPIUM BARBADENSE; GOSSYPIUM HIRSUTUM;

EID: 33847302543     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2006.04.0249     Document Type: Article

References (56)

1. Borevitz, J.O., D. Liang, D. Plouffe, H.S. Chang, T. Zhu, D. Weigel, C.C. Berry, E. Winzeler, and J. Chory. 2003. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13:513-523.
2. Calenge, F., C.G. van der Linden, E. van de Weg, H.J. Schouten, G. van Arkel, C. Denance, and C.E. Durel. 2005. Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple. Theor. Appl. Genet. 110:660-668.
3. Cantrell, R.G., and D.D. Davis, 2000. Registration of NM24016, an interspecific-derived cotton genetic stock. Crop Sci. 40:1208,
4. Chen, X.M., R.F. Line, and H. Leung. 1998. Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis. Theor. Appl. Genet. 97:345-355.
5. Clement, D., C. Lanaud, X. Sabau, O. Fouet, L. Le Cunff, E. Ruiz, A.M. Risterucci, J.C. Glaszmann, and P. Piffanelli. 2004. Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones. Theor. Appl. Genet. 108:1627-1634.
6. Collins, N.C., C.A. Webb, S. Seah, J.G. Ellis, S.H. Hulbert, and A. Pryor. 1998. The isolation and mapping of disease resistance gene analogs in maize. Mol. Plant Microbe Interact. 11:968-978.
7. Gaspero, G, and G. Cipriani. 2003. Nucleotide binding site/leucine-rich repeats, Pto-like and receptor-like kinases related to disease resistance in grapevine. Mol. Genet. Genomics 269:612-623.
8. Dilbirligi, M., M. Erayman, D. Sandhu, D. Sidhu, and K.S. Gill. 2004. Identification of wheat chromosomal regions containing expressed resistance genes. Genet. 166:461-481.
9. Egea-Gilabert, C., M.J. Dickinson, G. Bilotti, and M.E. Candela. 2003. Isolation of resistance gene analogs in pepper using modified AFLPs. Biol. Plant. 47:27-32.
10. Feuillet, C., G. Schachermayr, and B. Keller. 1997. Molecular cloning of a new receptor-like kinase gene encoded at the Lr10 disease resistance locus of wheat. Plant J. 11:45-52.
11. Fourmann, M., F. Chariot, N. Froger, R. Delourme, and D. Brunel. 2001. Expression, mapping, and genetic variability of Brassica napus disease resistance gene analogues. Genome 44:1083-1099.
12. Graham, M.A., L.F. Marek, and R.C. Shoemaker. 2002. Organization, expression and evolution of a disease resistance gene cluster in soybean. Genet. 162:1961-1977.
13. Grube, R.C., E.R. Radwanski, and M. Jahn. 2000. Comparative genetics of disease resistance within the Solanaceae. Genet. 155:873-887.
14. Hayes, A.J., and M.A. Saghai Maroof. 2000. Targeted resistance gene mapping in soybean using modified AFLPs. Theor. Appl. Genet. 100:1279-1283.
15. Hinchliffe, D.J., Y. Lu, C. Potenza, C. Segupta-Gopalan, R.G. Cantrell, and J.F. Zhang. 2005. Resistance gene analogue markers are mapped to homeologous chromosomes in cultivated tetraploid cotton. Theor. Appl. Genet. 110:1074-1085.
16. Hu, J., O.E. Ochoa, M.J. Truco, and B.A. Vick. 2005. Application of the TRAP technique to lettuce (Lactuca sativa L.) genotyping. Euphytica 144:225-235.
17. Hu, J., and B.A. Vick. 2003. TRAP (target region amplification polymorphism), a novel marker technique for plant genotyping. Plant Mol. Biol. Rep. 21:289-294.
18. Huettel, B., D. Santra, J. Muehlbauer, and G. Kahl. 2002. Resistance gene analogues of chickpea (Cicer arietinum L.): Isolation, genetic mapping and association with a Fusarium resistance gene cluster. Theor. Appl. Genet. 105:479-490.
19. Hunger, S., G. Di Gaspero, S. Mohring, D. Bellin, R. Schafer-Pregl, D.C. Borchardt, C.E. Durel, M. Werber, B. Weisshaar, F. Salamini, and K. Schneider. 2003. Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.). Genome 46:70-82.
20. Irigoyen, M.L., Y. Loarce, A. Fominaya, and E. Ferrer. 2004. Isolation and mapping of resistance gene analogs from the Avena strigosa genome. Theor. Appl. Genet. 109:713-724.
21. Kanazin, V., L.F. Marek, and R.C. Shoemaker. 1996. Resistance gene analogs are conserved and clustered in soybean. Proc. Natl. Acad. Sci. USA 93:11746-11750.
22. Kohel, R.J., T.R. Richmond, and C.F. Lewis. 1970. Texas Marker-1. Description of a genetic standard for Gossypium hirsutum L. Crop Sci. 10:670-671.
23. Kuhn, D.N., M. Heath, R.J. Wisser, A. Meerow, J.S. Brown, U. Lopes, and R.J. Schnell. 2003. Resistance gene homologues in Theobroma cacao as useful genetic markers. Theor. Appl. Genet. 107:191-202.
24. Leister, D., A. Ballvora, F. Salamini, and C. Gebhardt. 1996. A PCR-based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nat. Genet. 14:421-429.
25. Li, G., and C.F. Quiros. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: Its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103:455-461.
26. Liu, J.J., and A.K. Ekramoddoullah. 2003. Isolation, genetic variation and expression of TIR-NBS-LRR resistance gene analogs from western white pine (Pinus monticola Dougl. Ex. D. Don.). Mol. Genet. Genomics 270:432-441.
27. Liu, Z.H., J.A. Anderson, J. Hu, T.L. Friesen, J.B. Rasmussen, and J.D. Faris. 2005. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor. Appl. Genet. 111:782-794.
28. Mago, R., S. Nair, and M. Mohan. 1999. Resistance gene analogues in rice: Cloning, sequencing and mapping. Theor. Appl. Genet. 99:50-57.
29. Martin, G.B., A.J. Bogdanove, and G. Sessa. 2003. Understanding the functions of plant disease resistance proteins. Annu. Rev. Plant Physiol. Plant Mol. Biol. 54:23-61.
30. McIntyre, C.L., R.E. Casu, J. Drenth, D. Knight, V.A. Whan, B.J. Croft, D.R. Jordan, and J.M. Manners. 2005. Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance. Genome 48:391-400.
31. Meyers, B.C., A. Kozik, A. Griego, H. Kuang, and R.W. Michelmore. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15:809-834.
32. Monosi, B., R.J. Wisser, L. Pennill, and S.H. Hulbert. 2004. Full-genome analysis of resistance gene homologues in rice. Theor. Appl. Genet. 109:1434-1447.
33. Pan, Q., and J.F. Wendel. 2001. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50:203-213.
34. Penuela, S., D. Danesh, and N.D. Young. 2002. Targeted isolation, sequence analysis, and physical mapping of non-TIR NBS-LRR genes in soybean. Theor. Appl. Genet. 104:261-272.
35. Percy, R.G., R.G. Cantrell, and J.F. Zhang. 2006. Genetic variation for agronomic and fiber properties in an introgressed recombinant inbred population of cotton. Crop Sci. 46:1311-1317.
36. Quint, M., C.M. Dussle, A.E. Melchinger, and T. Lubberstedt. 2003. Identification of genetically linked RGAs by BAC screening in maize and implications for gene cloning, mapping and MAS. Theor. Appl. Genet. 106:1171-1177.
37. Radwan, O., M.F. Bouzidi, P. Nicolas, and S. Mouzeyar. 2004. Development of PCR markers for the P15/P18 locus for resistance to Plasmopara halstedii in sunflower, Helianthus annuus L. from complete CC-NBS-LRR sequences. Theor. Appl. Genet. 109:176-185.
38. Rajesh, P.N., C. Coyne, K. Meksem, K.D. Sharma, V. Gupta, and F.J. Muehlbauer. 2004. Construction of a HindIII Bacterial Artificial Chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor. Appl. Genet. 108:663-669.
39. Rossi, M., P.G. Araujo, F. Faulet, O. Garsmeur, V.M. Dias, H. Chen, M.A. Van Sluys, and A. D'Hont. 2003. Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol. Genet. Genomics 269:406-419.
40. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
41. Smith, C.W., H.S. Moser, R.G. Cantrell, and S.R. Oakley. 1999. History of cultivar development in the United States, p. 99-171. In C.W Smith and J.T. Cothren (ed.) Cotton: Origin, history, technology, and production. John Wiley & Sons, New York.
42. Soriano, J.M., S. Vilanova, C. Romero, G. Llacer, and M.L. Badenes. 2005. Characterization and mapping of NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.). Theor. Appl. Genet. 110:980-989.
43. Trognitz, F.Ch., and B.R. Trognitz. 2005. Survey of resistance gene analogs in Solanum caripense, a relative of potato and tomato, and update on R gene genealogy. Mol. Genet. Genomics 274:595-605.
44. Ulloa, M., S. Saha, J.N. Jenkins, W.R. Meredith, Jr., J.C. McCarty, Jr., and D.M. Stelly. 2005. Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.). Joinmap. J. Hered. 96:132-144.
45. van der Linden, C.G., D.C. Wouters, V. Mihalka, E.Z. Kochieva, M.J. Smulders, and B. Vosman. 2004. Efficient targeting of plant disease resistance loci using NBS profiling. Theor. Appl. Genet. 109:384-393.
46. van Leeuwen, H., J. Garcia-Mas, M. Coca, P. Puigdomenech, and A. Monfort. 2005. Analysis of the melon genome in regions encompassing TIR-NBS-LRR resistance genes. Mol. Genet. Genomics 273:240-251.
47. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabean. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414.
48. Weising, K., H. Nybom, K. Wolff, and G. Kahl. 2005. DNA finger-printing in plants: Principles, methods, and applications. 2nd edition. CRC Press, Boca Raton, FL.
49. Xiao, W., M. Xu, J. Zhao, F. Wang, J. Li, and J. Dai. 2006. Genome-wide isolation of resistance gene analogs in maize. Theor. Appl. Genet. 113:63-72.
50. You, M., J.G. Boersma, B.J. Buirchell, M.W Sweetingham, K.H. Siddique, and H. Yang. 2005. A PCR-based molecular marker applicable for marker-assisted selection for anthracnose disease resistance in lupin breeding. Cell. Mol. Biol. Lett. 10:123-134.
51. Yu, Y.G., G.R. Buss, and M.A. Maroof. 1996. Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc. Natl. Acad. Sci. USA 93:11751-11756.
52. Yuksel, B., J.C. Estill, S.R. Schulze, and A.H. Paterson. 2005. Organization and evolution of resistance gene analogs in peanut. Mol. Genet. Genomics 274:248-263.
53. Zhang, J.F., Y.Z. Lu, R.G. Cantrell, and E. Hughs. 2005a. Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the southwest USA. Crop Sci. 45:1483-1490.
54. Zhang, J.F., Y.Z. Lu, and S.X. Yu. 2005b. Cleaved AFLP (cAFLP), a modified amplified fragment length polymorphism analysis for cotton. Theor. Appl. Genet. 111:1385-1395.
55. Zhang, J.F., and J.M. Stewart. 2000. Economic and rapid method for extracting cotton genomic DNA. J. Cotton Sci. 4:193-201.
56. Zhang, Z., J. Xu, Q. Xu, P. Larkin, and Z. Xin. 2004. Development of novel PCR markers linked to the BYDV resistance gene Bdv2 useful in wheat for marker-assisted selection. Theor. Appl. Genet. 109:433-439.