Genetic relationship in Coffea species and parentage determination of interspecific hybrids using ISSR (Inter-Simple Sequence Repeat) markers

Genetics and Molecular Biology

Volumn 26, Issue 3, 2003, Pages 319-327

  Ruas, Paulo M ^a   Ruas, Claudete F ^a   Rampim, Leandro ^a   Carvalho, Valdemar P ^a   Ruas, Eduardo A ^b   Sera, Tumoru ^b  

^a STATE UNIVERSITY OF LONDRINA   (Brazil)

^b INSTITUTO AGRONÔMICO DO PARANÁ   (Brazil)

Author keywords

Coffea; Coffee breeding; DNA markers; ISSR

Indexed keywords

ADENINE; DINUCLEOTIDE; DNA FRAGMENT; GUANINE; MICROSATELLITE DNA; NUCLEOTIDE DERIVATIVE; PRIMER DNA; TRINUCLEOTIDE;

ARTICLE; CLUSTER ANALYSIS; COFFEE; CONTROLLED STUDY; DNA POLYMORPHISM; GENE AMPLIFICATION; GENE FREQUENCY; GENE SEQUENCE; GENETIC MARKER; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOME ANALYSIS; INTERSPECIFIC HYBRID; MOLECULAR PHYLOGENY; NONHUMAN; PARENTAGE ANALYSIS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION;

COFFEA; COFFEA ARABICA; COFFEA LIBERICA; COFFEA LIBERICA VAR. DEWEVREI; COFFEA RACEMOSA;

EID: 0142211130     PISSN: 14154757     EISSN: None     Source Type: Journal    
DOI: 10.1590/S1415-47572003000300017     Document Type: Article

References (48)

1. Ajibade SR, Weeden NF and Chite SM (2000) Inter simple sequence repeat analysis of genetic relationship in the genus Vigna. Euphytica 111:47-55.
2. Akagi H, Yokozeki Y, Inagaki A and Fugimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94:61-67.
3. Anthony F, Bertrand B, Quiros O, Wilches A, Lachermes P, Berthaud J and Charrier A (2001) Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers. Euphytica 118:53-65.
4. Berthaud J and Charrier A (1988) Genetic Resources of Coffea. In: Clarke RJ, Macrae R (eds) Coffea Agronomy, Elsevier Applied Science Publishers, Paris, pp 1-42.
5. Berthou F and Trouslot P (1977) L'analyse en électrophorère du polymorphisme enzymatique dans le genre Coffea: adaptation d'une méthod d'életrophorèse en serie. 8th Int Sci Colloquium on coffee, Paris, France.
6. Berthou F, Mathieu C and Vedel F (1983) Chloroplast and mitochondrial DNA variation as indicator of phylogenetic relationship in genus Coffea L. Theor Appl Genet 65:77-84.
7. Berthou F, Trouslot P, Hamon S, Vedel F and Ouetier F (1980) Analyse en électrophorèse du polymorphisme biochimique des caféiers: variation enzymatique dans dix-huit populations sauvages: C. canephora, C. eugenioides et C. arabica. Café Cacao Thé 624:313-326.
8. Blair MW, Panaud O and McCouch SR (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.) Theor Appl Genet 98:780-792.
9. Botstein D, White RL, Skolnick M and Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-321.
10. Carvalho A (1946) Distribuição-geográfica e classificação botânica do gênero Coffea com referência especial à espécie Arabica. Boletim da Superinteridência dos Serviços do Café 21:174-180.
11. Carvalho A and Monaco LC (1962) Natural cross pollination in Coffea arabica. Proc. XVI Intern Hort Congr, Brussels, Belgium.
12. Charrier A (1978) La structure genetique des caféiers spontanés de la région Malgashe (Mascarocoffea), leurs relations avec les caféiers d'origine africaine (Eucoffea). Memoires ORSTOM, Paris, 224 pp.
13. Charrier A and Berthaud J (1985) Botanical classification of coffee. In: Clifford MN and Willson KC (eds) Coffee, Botany, Biochemistry and Production of beans and beverage. Croom Helm, London, pp 13-47.
14. Chin ECL, Senior ML, Shu H and Smith JSC (1996) Maize simple repetitive DNA sequences abundance and allele variation. Genome 39:886-873.
15. Coelho ASG (2001) BOOD - Avaliação de dendrogramas baseados em estimativas de distâncias/similaridades genéticas através do procedimento de bootstrap, Versão 3.0. Departamento de Biologia Geral, Instituto de Ciêcias Biológicas, Universidade Federal de Goiás, Goiânia, GO.
16. Coelho ASG (2001) DBOOT - Avaliação dos erros associados a estimativas de distâncias/similaridades genéticas através do procedimento de bootstrap com número variável de marcadores, Versão 1.1. Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO.
17. Depeiges A, Golbely C, Lenoir A, Cocherel S, Picard G, Raynal M, Grellet F and Delseny M (1995) Identification of the most represented repeated motif in Arabidopsis thaliana microsatellite loci. Theor Appl Genet 91:160-168.
18. Dow BD, Ashley MV and Hove HF (1995) Characterization of highly variable (GA/CT)n microsatellite in the burr oak, Quercus macrocarpa. Theor Appl Genet 91:137-141.
19. Doyle J J and Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytoch Bull 19:11-15.
20. Dublin P, Enjalrik F, Lardet L, Carron MP, Troulinder N and Pannetier C (1991) Estate crops. In: Debergh PC and Zimmerman RH (eds) Micropopagation: Technology and practice, Kluwer Academic Publ, Dordrecht, pp 337-361.
21. Fazuoli LC, Maluf MP, Guerreiro-Filho O, Medina-Filho HP and Silvarolla MB (2000) Breeding and biotechnology of coffee. In: Sera T, Soccol CR, Pandey A and Roussos S (eds) Coffee Biotechnology and Quality, Kluwer Academic Publishers, Dordrecht, pp 27-45.
22. Felsenstein J (1985) Confidence Limits on Phylogenies: an Approach Using the Bootstrap. Evolution 39(4):783-791.
23. Goodwin ID, Aiktken EAB and Smith LW (1997) Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18:1524-1528.
24. Gupta M, Chyi YS, Romero-Severson J and Owen JL (1994) Amplification of DNA markers from evolutionarily diverse genome using single primers of simple-sequence repeats. Theor Appl Genet 89:998-1006.
25. Hantula J, Dusabenygasani M and Hamelin RC (1996) Random amplified microsatellites (RAMS) - a novel method for characterizing genetic variation within fungi. Eur J For Path 26:15-166.
26. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Wiel C van de, Bredemeijer G, Vosman B, Matthes M, Maly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi R, Marmiroli N, Aert R, Volckaert G, JRueda J, Linaacero R, Vazque A and Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breeding 3:381-390.
27. Kantety RV, Zeng X, Bebbetzen JL and Zehr BE (1995) Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbreed lines using inter-simple sequence repeat (ISSR) amplification. Mol Breeding 1:36-373.
28. Lashermes P, Combes MC, Roberts J, Trouslot P, D'Hont A, Anthony F and Charrier A (1999) Molecular characterization and origin of the Coffea arabica L. genome. Molec Gen Genet 261:259-266.
29. Lashermes P, Combes MC, Trouslot P and Charrier A (1997) Phylogenctic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet 94:947-955.
30. Lashermes P, Cros J, Combes MC, 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.
31. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:299-220.
32. McGregor CE, Lambert CA, Greyling MM, Louw JH and Warnich LA (2000) comparative assessment of DNA finger-printing techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.). Euphytica 113:135-144.
33. Michelmore RW, Paran I and Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828-9832.
34. Morgante M and Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. The Plant J 3:175-182.
35. Nagaoka T and Ogihara Y (1997) Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor Appl Genet 94:597-602.
36. Orozco-Castillo C, Charmers KJ and Powell RW (1994) Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theor Appl Genet 87:934-940.
37. Paillard M, Lashermes P and Pétrard V (1996) Construction of a molecular linkage maps in coffee. Theor Appl Genet 93:41-47.
38. Raina SN, Mukai Y and Yamamoto M (1998) In situ hybridization identifies the diploid progenitor species of Coffea arabica (Rubiaceae). Theor Appl Genet 97:1204-1209.
39. Rohlf FJ (2000) NTSYS-pc Numerical Taxonomy and Multivariate Analysis System version 2.1. Owner manual.
40. Ruas PM, Diniz LEC, Ruas CF and Sera T (2000) Genetic Polymorphism in species and hybrids of Coffea revealed by RAPD. In: Sera T, Soccol CR, Pandey A, Roussos S (eds) Coffee Biotechnology and Quality. Kluwer Academic Publishers, Dordrecht, pp 187-195
41. Sneath PHA and Sokal RR (1973) Numerical taxonomy. Freeman. San Francisco, 573 pp.
42. Van der Vossen HAM (1985) Coffee selection and breeding In: Clifford MN and Willson KC (eds) Coffee: Botany, Biochemistry and Production of Beans and Beverage. Croom Helm, London, p 48-96.
43. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Fritjers A, Pot J, Peleman J, Kuiper M and Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Ac Res 23:4407-4414.
44. Wang, Z, Weber JL, Zhong G and Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1-6.
45. Welsh J and McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids 18:7213-7218.
46. Williams JGK, Kubelik AR, Livak KJ and Rafalski JA (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Ac Res 18:6531-6535.
47. Wriglei G (1995) Coffee. In: Smartt J and Simmonds NW (eds) Evolution of crop plants. Longman Scientific and Technical, London, pp 438-443.
48. Zietkiewics E, Rafalski A and Labuda D (1994) Genome fingerprint by sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176-183.