Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta

Genome

Volumn 50, Issue 12, 2007, Pages 1078-1088

  López, Camilo E ^a,c   Quesada Ocampo, Lina M ^b,d   Bohórquez, Adriana ^b   Duque, Myriam Cristina ^b   Vargas, Jaime ^b   Tohme, Joe ^b   Verdier, Valérie ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

^c UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^d MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Cassava; Cassava bacterial blight resistance; EST; QTL mapping; SSR

Indexed keywords

BIOLOGICAL MARKER;

ALLELE; ARTICLE; CASSAVA; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; GENE; GENETICS; GENOTYPE; IMMUNOLOGY; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PLANT DISEASE; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT; XANTHOMONAS;

ALLELES; BASE SEQUENCE; BIOLOGICAL MARKERS; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENES, PLANT; GENOTYPE; MANIHOT; MINISATELLITE REPEATS; PLANT DISEASES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; XANTHOMONAS;

EID: 40949151644     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G07-087     Document Type: Article

References (41)

1. Basten, C.J., Weir, B.S., and Zeng, Z.-B. 1999. QTL Cartographer. Department of Statistics, North Carolina State University, Raleigh, N.C.
2. Cardle, L., Ramsay, L., Milbourne, D., Macaulay, M., Marshall, D., and Waugh, R. 2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 156: 847-854. 11014830
3. Dellaporta, S.L., Wood, J., and Hicks, J.B. 1983. A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1: 19-21.
4. FAO. 2004. Cassava. In Food outlook. Food and Agriculture Organization of the United Nations, Rome.
5. Fofana, I.B.F., Sangare, A., Collier, R., Taylor, C., and Fauquet, C.M. 2004. A geminivirus-induced gene silencing system for gene function validation in cassava. Plant Mol. Biol. 56: 613-624. 10.1007/s11103-004-0161-y 15630624
6. Fregene, M., Angel, F., Gómez, R., Rodríguez, F., Chavarriaga, P., Roca, W., Tohme, J., and Bonierbale, M. 1997. A molecular genetic map of cassava Manihot esculenta Crantz. Theor. Appl. Genet. 95: 431-441. 10.1007/s001220050580
7. Gonzalo, M.J., Oliver, M., García-Mas, J., Monfort, A., Dolcet-Sanjuan, R., Katzir, N., Arus, P., and Monforte, A.J. 2005. Simple-sequence repeat markers used in merging linkage maps of melon Cucumis melo L. Theor. Appl. Genet. 110: 802-811. 10.1007/s00122-004-1814-6 15700148
8. Hahn, S.K., Howland, A.K., and Terry, E. 1980. Correlated resistance of cassava to mosaic and bacterial blight diseases. Euphytica, 29: 305-311. 10.1007/BF00025127
9. Jorge, V., Fregene, M.A., Duque, M.C., Bonierbale, M.W., Tohme, J., and Verdier, V. 2000. Genetic mapping of resistance to bacterial blight disease in cassava Manihot esculenta Crantz. Theor. Appl. Genet. 101: 865-872. 10.1007/s001220051554
10. Jorge, V., Fregene, M., Vélez, C.M., Duque, M.C., Tohme, J., and Verdier, V. 2001. QTL analysis of field resistance to Xanthomonas axonopodis pv. manihotis in cassava. Theor. Appl. Genet. 102: 564-571. 10.1007/s001220051683
11. Kosambi, D.D. 1944. The estimation of map distance from recombination values. Ann. Eugen. 12: 172-175.
12. Kpemoua, K., Boher, B., Nicole, M., Calatayud, P., and Geiger, J.P. 1996. Cytochemistry of defense responses in cassava infected by Xanthomonas campestris pv. manihotis. Can. J. Microbiol. 42: 1131-1143.
13. La Rota, M., Kantety, R.V., Yu, J.K., and Zorreéis, M.E. 2005. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics, 6: 23. 10.1186/1471-2164-6-23 15720707
14. Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., and Newburg, L. 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1: 174-181. 10.1016/0888-7543(87)90010-3 3692487
15. Lopez, C.E., Zuluaga, A.P., Cooke, R., Delseny, M., Tohme, J., and Verdier, V. 2003. a. Isolation of resistance gene candidates (RGCs), and characterization of an RGC cluster in cassava. Mol. Genet. Genomics, 269: 658-671. 10.1007/s00438-003-0868-5 12827500
16. Lopez, C.E., Acosta, I.F., Jara, C., Pedraza, F., Gaitán-Solis, E., Gallego, G., Beebe, S., and Tohme, J. 2003. b. Identifying resistance gene analogs associated with resistances to different pathogens in common bean. Phytopathology, 93: 88-95. 10.1094/PHYTO.2003.93.1.88
17. Lopez, C., Jorge, V., Piégu, B., Mba, C., Cortes, D., Restrepo, S., et al. 2004. A unigene catalogue of 5700 expressed genes in cassava. Plant Mol. Biol. 56: 541-554. 10.1007/s11103-004-0123-4 15630618
18. Lopez, C., Soto, M., Restrepo, S., Piégu, B., Cooke, R., Delseny, M., et al. 2005. a. Gene expression profile in response to Xanthomonas axonopodis pv. manihotis infection in cassava using a cDNA microarray. Plant Mol. Biol. 57: 393-410. 10.1007/s11103-004-7819-3 15830129
19. Lopez, C., Piégu, B., Cooke, R., Delseny, M., Tohme, J., and Verdier, V. 2005. b. Using cDNA and genomic sequences as tools to develop SNP strategies in cassava Manihot esculenta Crantz. Theor. Appl. Genet. 110: 425-431. 10.1007/s00122-004-1833-3 15650816
20. Lozano, J.C., and Sequeira, L. 1974. Bacterial blight of cassava in Colombia. Phytopathology, 64: 74-81.
21. Mba, R.E.C., Stephenson, P., Edwards, K., Melzer, S., Nkumbira, J., Gullberg, U., et al. 2001. Simple sequence repeat SSR markers survey of the cassava Manihot esculenta Crantz. genome: towards an SSR-based molecular genetic map of cassava. Theor. Appl. Genet. 102: 21-31. 10.1007/s001220051614
22. Morgante, M., Hanafey, M., and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200. 10.1038/ng822 11799393
23. Nicot, N., Chiquet, V., Gandon, B., Amilhat, L., Legeai, F., Leroy, P., et al. 2004. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor. Appl. Genet. 109: 800-805. 10.1007/s00122-004-1685- x 15146317
24. Pflieger, S., Lefebvre, V., Caranta, C., Blattes, A., Goffinet, B., and Palloix, A. 1999. Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions. Genome, 42: 1100-1110. 10.1139/gen-42-6-1100 10659776
25. Ramalingam, J., Vera-Cruz, C.M., Kukreja, K., Chittoor, J.M., Wu, J.L., Lee, S.W., et al. 2003. Candidate defense genes from rice, barley and maize and their association with qualitative and quantitative resistance in rice. Mol. Plant Microbe Interact. 16: 14-24. 10.1094/MPMI.2003.16.1.14 12580278
26. Restrepo, S., and Verdier, V. 1997. Geographical differentiation of the population of Xanthomonas axonopodis pv. manihotis in Colombia. Appl. Environ. Microbiol. 63: 4427-4434. 16535731
27. Restrepo, S., Duque, M.C., Tohme, J., and Verdier, V. 1999. AFLP fingerprinting: an efficient technique for detecting genetic variation of Xanthomonas axonopodis pv. manihotis. Microbiology, 145: 107-114. 10206688
28. Restrepo, S., Duque, M.C., and Verdier, V. 2000. Characterization of pathotypes among isolates of Xanthomonas axonopodis pv. manihotis in Colombia. Plant Pathol. 49: 680-687. 10.1046/j.1365-3059.2000.00513.x
29. Rozen, S., and Skaletsky, H.J. 2000. Primer3 on the WWW for general users and for biologist programmers. Humana Press, Totowa, N.J.
30. Rudd, S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci. 8: 321-329. 10.1016/S1360-1385(03) 00131-6 12878016
31. Rungis, D., Berube, Y., Zhang, J., Ralph, S., Ritland, C.E., Ellis, B.E., et al. 2004. Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor. Appl. Genet. 109: 1283-1294. 10.1007/s00122-004-1742-5 15351929
32. Sánchez, G., Restrepo, S., Duque, M.C., Fregene, F., Bonierbale, M., and Verdier, V. 1999. AFLP assessment of genetic variability in cassava accessions (Manihot esculenta) resistant and susceptible to the cassava bacterial blight (CBB). Genome, 42: 163-172.
33. Shaner, G., and Finney, R.E. 1977. The effect of nitrogen fertilization on the expression of slow-mildewing resistance in Knox wheat. Phytopathology, 67: 1051-1056.
34. Tanksley, S.D., and McCouch, S.R. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science (Washington, D.C.), 277: 1063-1066. 10.1126/science.277.5329.1063 9262467
35. Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., and McCouch, S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. 10.1101/gr.184001 11483586
36. Thiel, T., Kota, R., Grosse, I., Stein, N., and Graner, A. 2004. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res. 32: e5. 10.1093/nar/gnh006 14704362
37. Tomkins, J., Fregene, M., Main, D., Wing, R., and Tohme, J. 2004. Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava Manihot esculenta Crantz. Plant Mol. Biol. 56: 555-561. 10.1007/s11103-004-5045-7 15630619
38. Varshney, R.K., Graner, A., and Sorrells, M.E. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48-55. 10.1016/j.tibtech.2004.11.005 15629858
39. Verdier, V., Boher, B., Maraite, H., and Geiger, J.P. 1994. Pathological and molecular characterization of Xanthomonas campestris strains causing diseases of cassava Manihot esculenta. Appl. Environ. Microbiol. 60: 4478-4486. 16349463
40. Verdier, V., Restrepo, S., Mosquera, G., Jorge, V., and López, C.E. 2004. Recent progress in the characterization of molecular determinants in the Xanthomonas axonopodis pv. manihotis-cassava interaction. Plant Mol. Biol. 56: 573-584. 10.1007/s11103-004-5044-8 15630621
41. Wydra, K., Zinsou, V., Jorge, V., and Verdier, V. 2004. Identification of pathotypes of Xanthomonas axonopodis pv. manihotis in Africa and detection of quantitative trait loci and markers for resistance to bacterial blight of cassava. Phytopathology, 94: 1084-1093. 10.1094/PHYTO.2004.94.10.1084