Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Genome

Volumn 50, Issue 7, 2007, Pages 619-626

  Herrera, Juan Carlos ^a   D'Hont, Angelique ^b   Lashermes, Philippe ^c  

^a Centro Nacional de Investigaciones de Cafe   (Colombia)

^b CIRAD   (France)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

BAC FISH; Coffee; Genome evolution; GISH; Interspecific hybridization; Introgression

Indexed keywords

PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLASSIFICATION; COFFEE; CROSS BREEDING; EVALUATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GENOME; METABOLISM; PLANT CHROMOSOME;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; COFFEA; CROSSES, GENETIC; DNA, PLANT; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE;

COFFEA ARABICA;

EID: 34948896917     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G07-034     Document Type: Article

References (40)

1. Agwanda, C., Lashermes, P., Trouslot, P., Combes, M.C., and Charrier, A. 1997. Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in Arabica coffee. Euphytica, 97: 241-248. doi:10.1023/A:1003097913349.
2. Anamthawat-Jónsson, K. 2001. Molecular cytogenetics of introgressive hybridization in plants. Methods Cell Sci. 23: 139-148.
3. Barre, P., Laissac, M., D'Hont, A., Louarn, J., Charrier, A., Hamon, S., and Noirot, M. 1998. Relationship between parental chromosomic contribution and nuclear DNA content in the coffee interspecific hybrid C. pseudozanguebariae x C. liberica var 'dewevrei'. Theor. Appl. Genet. 96: 301-305. doi:10.1007/s001220050740.
4. Berthaud, J. 1978. L'hybridation interspécifique entre Coffea arabica L. et Coffea canephora Pierre. Obtention et comparaison des hybrides triploïdes, arabusta et hexaploïdes. Cafe Cacao The, 22: 87-109.
5. Bettencourt, A.J., and Rodrigues, C.J., Jr. 1988. Principles and practice of coffee breeding for resistance to rust and other diseases. In Coffee, Vol. 4: Agronomy. Edited by R.J. Clarke and R. Macrae. Elsevier Applied Science, London. pp. 199-234.
6. Bouharmont, J. 1959. Recherches sur les affinités chromosomiques dans le genre Coffea. Publ. INEAC, Série Scientifique, 77.
7. Charrier, A., and Berthaud, J. 1985. Botanical classification of coffee. In Coffee: Botany, biochemistry and production of beans and beverage. Edited by M.N. Clifford and K.C. Willson. Croom Helm Ltd., UK. pp. 13-47.
8. Cramer, P.J.S. 1957. A review of literature of coffee research in Indonesia. SIC Ed., IICA, Turrialba, Costa Rica.
9. Cronn, R.C., Small, R.L., and Wendel, J.F. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proc. Natl. Acad. Sci. U.S.A. 96: 14406-14411. doi:10.1073/pnas.96. 25.14406.
10. Cros, J., Combes, M.C., Trouslot, P., Anthony, F., Hamon, S., Charrier, A., and Lashermes, P. 1998. Phylogenetic analysis of chloroplast DNA variation in Coffea L. Mol. Phylogenet. Evol. 9: 109-117. doi:10.1006/mpev.1997.0453.
11. D'Hont, A., Paget-Goy, A., Escoute, J., and Carreel, F. 2000. The interspecific genome structure of cultivated banana, Musa spp. revealed by genomic DNA in situ hybridization. Theor. Appl. Genet. 100: 177-183. doi:10.1007/s001220050024.
12. Fahlesen, J., Lagercrantz, U., Monras, A., and Glimelius, K. 1997. Characterization of somatic hybrids between Brassica napus and Eruca sativa using species specific sequences and genomic in situ hybridization. Plant Sci. 123: 133-142.
13. Hans de Jong, J., Fransz, P., and Zabel, P. 1999. High resolution FISH in plants - techniques and applications. Trends Plant Sci. 4: 258-263. doi:10.1016/S1360-1385(99)01436-3.
14. Herrera, J.C., Combes, M.C., Anthony, F., Charrier, A., and Lashermes, P. 2002. Introgression into the allotetraploid coffee (Coffea arabica L.): Segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid (C. arabica x C. canephora). Theor. Appl. Genet. 104: 661-668. doi:10.1007/s001220100747.
15. Jiang, J., and Gill, B.S. 1994. Nonisotopic in situ hybridization and plant genome mapping: the first 10 years. Genome, 37: 717-725.
16. Jiang, J., Gill, B.S., Wang, G.-L., Ronald, P., and Ward, D.C. 1995. Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc. Natl. Acad. Sci. U.S.A. 92: 4487-4491. doi:10.1073/pnas.92.10.4487.
17. Kamm, A., Galasso, I., Schmidt, T., and Heslop-Harrison, J.S. 1995. Analysis of a repetitive DNA family from Arabidopsis arenosa and relationship between Arabidopsis species. Plant Mol. Biol. 27: 853-862. doi:10.1007/BF00037014.
18. Kim, J.-S., Childs, K.L., Islam-Faridi, M.N., Menz, M.A., Klein, R.R., Klein, P.E., et al. 2002. Integrated karyotyping of sorgum by in situ hybridization of landed BACs. Genome, 45: 402-412. doi:10.1139/g01-141.
19. Lashermes, P., Cros, J., Combes, M.C., Trouslot, P., Anthony, F., Hamon, S., and Charrier, A. 1996. Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. Theor. Appl. Genet. 93: 626-632.
20. Lashermes, P., Combes, M.C., Trouslot, P., and Charrier, A. 1997. Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor. Appl. Genet. 94: 947-955. doi:10.1007/s001220050500.
21. Lashermes, P., Combes, M.C., Robert, J., Trouslot, P., D'Hont, A., Anthony, F., and Charrier, A. 1999. Molecular characterisation and origin of the Coffea arabica L. genome. Mol. Gen. Genet. 261: 259-266.
22. Lashermes, P., Paczek, V., Trouslot, P., Combes, M.C., Couturon, E., and Charrier, A. 2000. Single-locus inheritance in the allotetraploid Coffea arbica L. and interspecific hybrid C. arabica x C. canephora. J. Hered. 91: 81-85. doi:10.1093/jhered/91.1.81.
23. Lashermes, P., Combes, M.C., Prakash, N.S., Trouslot, P., Lorieux, M., and Charrier, A. 2001. Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meiosis. Genome, 44: 589-596. doi:10.1139/gen-44-4-589.
24. Lim, K.Y., Leitch, I.J., and Leitch, A.R. 1998. Genomic characterization and the detection of raspberry chromatin in polyploid Rubus. Theor. Appl. Genet. 97: 1027-1033. doi:10.1007/s001220050987.
25. Lin, C., Mueller, L.A., McCarthy, J., Crouzillat, D., Pétiard, V., and Tanksley, S.D. 2005. Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor. Appl. Genet. 112: 114-130. doi:10.1007/s00122-005-0112-2.
26. Liu, B., Brubaker, C.L., Mergeai, G., Cronn, R.C., and Wendel, J.F. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome, 44: 321-330. doi:10.1139/gen-44-3-321.
27. Mahé, L. 2006. Contribution à l'amélioration génétique de la résistance des caféiers (Coffea arabica) à la rouille (Hemileia vastatrix): De l'étude des hybrides interspécifiques naturels de Nouvelle-Calédonie à la cartographie d'un locus de résistance. Ph.D. thesis, Agro.M, Montpellier, France.
28. Noir, S., Patheyron, S., Combes, M.C., and Lashermes, P. 2004. Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.). Theor. Appl. Genet. 109: 225-230.
29. Pinto-Maglio, C.A.F., and Da Cruz, N.D. 1998. Pachytene chromosome morphology in Coffea L. II. C. arabica L. complement. Caryologia, 51: 19-35.
30. Prakash, N.S., Combes, M.C., Somanna, N., and Lashermes, P. 2002. AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica, 124: 265-271. doi:10.1023/A:1015736220358.
31. Prakash, N.S., Marques, D.V., Varzea, V.M., Silva, M.C., Combes, M.C., and Lashermes, P. 2004. Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into C. arabica L. Theor. Appl. Genet. 109: 1311-1317. doi:10.1007/s00122-004-1748-z.
32. Puertas, M., and Naranjo, T. (Editors). 2005. Plant cytogenetics. Karger, Basel, Switzerland.
33. Raina, S.N., and Rani, V. 2001. GISH technology in plant genome research. Methods Cell Sci. 23: 83-104. doi:10.1023/A:1013197705523.
34. Rieseberg, L.H., Baird, S.J.E., and Gardner, K.A. 2000. Hybridization, introgression, and linkage evolution. Plant Mol. Biol. 42: 205-224. doi:10.1023/A:1006340407546.
35. Rodrigues, C.J., Jr., Bettencourt, A.J., and Rijo, L. 1975. Races of the pathogen and resistance to coffee rust. Annu. Rev. Phytopathol. 13: 49-70. doi:10.1146/annurev.py.13.090175.000405.
36. Schmidt, T., and Heslop-Harrison, J.S. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci. 3: 195-199. doi:10.1016/S1360-1385(98)01223-0.
37. Schubert, I., Fransz, P.F., Fuchs, J., and Hans de Jong, J. 2001. Chromosome painting in plants. Methods Cell Sci. 23: 57-69. doi:10.1023/A:1013137415093.
38. Simmonds, N.W. 1993. Introgression and incorporation strategies for the use of crop genetic resources. Biol. Rev. 68: 539-562.
39. Van der Vossen, H.A.M. 2001. Coffee breeding practices. In Coffee: recent developments. Edited by R.J. Clarke and O.G. Vitzthum. Blackwell Science, Oxford. pp. 184-201.
40. Vishveshwara, S. 1974. Periodicity of Hemileia in arabica selection. Indian Coffee, 38: 49-51.