A platform for efficient genotyping in musa using microsatellite markers

AoB PLANTS

Volumn 11, Issue 1, 2011, Pages

  Christelová, Pavla ^a   Valárik, Miroslav ^a   Hřibová, Eva ^a   Van den houwe, Ines ^b   Channelière, Stéphanie ^c   Roux, Nicolas ^c   Doležel, Jaroslav ^a  

^a INSTITUTE OF EXPERIMENTAL BOTANY   (Czech Republic)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c BIOVERSITY INTERNATIONAL   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84879199231     PISSN: None     EISSN: 20412851     Source Type: Journal    
DOI: 10.1093/aobpla/plr024     Document Type: Article

References (64)

1. Bartoš J, Alkhimova O, Doleželová M, De Langhe E, Doležel J. 2005. Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications. Cytogenetic and Genome Research 109: 50-57.
2. Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P. 2004. How to track and assess genotyping errors in population genetic studies. Molecular Ecology 13: 3261-3273.
3. Bredemeijer GMM, Cooke R, Ganal M, Peeters R, Isaac P, Norordijk Y, Rendell S, Jackson J, Röder MS, Wendehake K, Dijcks M, Amelaine M, Wickaert V, Bertrand L, Vosman B. 2002. Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theoretical and Applied Genetics 105: 1019-1026.
4. Buhariwalla HK, Jarret RL, Jayashree B, Crouch JH, Ortiz R. 2005. Isolation and characterization of microsatellite markers from Musa balbisiana. Molecular Ecology Notes 5: 327-330.
5. Cheesman EE. 1947. Classification of the bananas II. The genus Musa L. Kew Bulletin 2: 106-117.
6. Cipriani G, Frazza G, Peterlunger E, Testolin R. 1994. Grapevine fingerprinting using microsatellite repeats. Vitis 33: 211-215.
7. Creste S, Neto AT, Silva SD, Figueira A. 2003. Genetic characterization of banana cultivars (Musa spp.) from Brazil using microsatellite markers. Euphytica 132: 259-268.
8. Crouch HK, Crouch JH, Jarret RL, Cregan PB, Ortiz R. 1998. Segregation of microsatellite loci in haploid and diploid gametes of Musa. Crop Science 38: 211-217.
9. Crouch HK, Crouch JH, Madsen S, Vuylsteke DR, Ortiz R. 2000. Comparative analysis of phenotypic and genotypic diversity among plantain landraces (Musa spp., AAB group). Theoretical and Applied Genetics 101: 1056-1065.
10. De Langhe E, Pillay M, Tenkouano A, Swennen R. 2005. Integrating morphological and molecular taxonomy in Musa: the African plantains (Musa spp. AAB group). Plant Systematics and Evolution 255: 225-236.
11. Doležel J. 1991. Flow cytometric analysis of nuclear DNA content in higher plants. Phytochemical Analysis 2: 143-154.
12. Doleželová M, Doležel J, Van den houwe I, Roux N, Swennen R. 2005. Focus on the Musa collection: ploidy levels revealed. Info- Musa 14: 34-36.
13. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. Plos One 6: e19379.
14. Esselink GD, Smulders MJ, Vosman B. 2003. Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theoretical and Applied Genetics 106: 277-286.
15. Gawel NJ, Jarret RL, Whittemore AP. 1992. Restriction fragment length polymorphism (RFLP)-based phylogenetic analysis of Musa. Theoretical and Applied Genetics 84: 286-290.
16. Grapin A, Noyer JL, Carreel F, Dambier D, Baurens FC, Lanaud C, Lagoda PJL. 1998. Diploid Musa acuminata genetic diversity assayed with sequence-tagged microsatellite sites. Electrophoresis 19: 1374-1380.
17. Hayden MJ, Nguyen TM, Waterman A, McMichael GL, Chalmers KJ. 2007. Application of multiplex-ready PCR for fluorescencebased SSR genotyping in barley and wheat. Molecular Breeding 21: 271-281.
18. Hippolyte I, Bakry F, Seguin M, Gardes L, Rivallan R, Risterucci AM, Jenny C, Perrier X, Carreel F, Argout X, Piffanelli P, Khan IA, Miller RNG, Pappas GJ, Mbéguié-A-Mbéguié D, Matsumoto T, De Bernardinis V, Huttner E, Kilian A, Baurens FC, D'Hont A, Cote1 F, Courtois B, Glaszmann JC. 2010. A saturated SSR/ DArT linkage map of Musa acuminata addressing genome rearrangements among bananas. BMC Plant Biology 10: 65.
19. Hřibová E, Čížková J, Christelová P, Taudien S, de Langhe E, Doležel J. 2011. The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny. PLoS ONE 6: e17863.
20. INIBAP. 2006. Global conservation strategy for Musa (Banana and Plantain). A consultative document prepared by INIBAP with the colaboration of numerous partners in the Musa research-and-development community. France: INIBAP.
21. Jarret RL, Gawel NJ. 1995. Molecular markers, genetic diversity and systematics. In: Gowen S, ed. Bananas and plantains. London: Chapman & Hall, 67-83.
22. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A. 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding 3: 381-390.
23. Kaemmer D, Fischer D, Jarret RL, Baurens FC, Grapin A, Dambier D, Noyer JL, Lanaud C, Kahl G, Lagoda PJL. 1997. Molecular breeding in the genus Musa: a strong case for STMS marker technology. Euphytica 96: 49-63.
24. Lagoda PJL, Noyer JL, Dambier D, Baurens FC, Grapin A, Lanaud C. 1998. Sequence tagged microsatellite site (STMS) markers in the Musaceae. Molecular Ecology 7: 657-666.
25. Li LF, Häkkinen M, Yuan YM, Hao G, Ge XJ. 2010. Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa. Molecular Phylogenetics and Evolution 57: 1-10.
26. Liu AZ, Kress WJ, Li DZ. 2010. Phylogenetic analyses of the banana family (Musaceae) based on nuclear ribosomal (ITS) and chloroplast (trnL-F) evidence. Taxon 59: 20-28.
27. Liu K, Muse SV. 2005. PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
28. Loh JP, Kiew R, Set O, Gan LH, Gan YY. 2000. Amplified fragment length polymorphism fingerprinting of 16 banana cultivars (Musa cvs.). Molecular Phylogenetics and Evolution 17: 360-366.
29. Lysák MA, Doleželová M, Horry JP, Swennen R, Doležel J. 1999. Flow cytometric analysis of nuclear DNA content in Musa. Theoretical and Applied Genetics 98: 1344-1350.
30. McKelvey KS, Schwartz MK. 2004. Genetic errors associated with population estimation using non-invasive molecular tagging: problems and new solutions. Journal of Wildlife Management 68: 439-448.
31. Michener CD, Sokal RR. 1957. A quantitative approach to a problem of classification. Evolution 11: 490-499.
32. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the USA 70: 3321-3323.
33. Ning SP, Xu LB, Lu Y, Huang BZ, Ge XJ. 2007. Genome composition and genetic diversity of Musa germplasm from China revealed by PCR-RFLP and SSR markers. Scientia Horticulturae 114: 281-288.
34. Nwakanma DC, Pillay M, Okoli BE, Tenkouano A. 2003. PCR-RFLP of the ribosomal DNA internal transcribed spacers (ITS) provides markers for the A and B genomes in Musa L. Theoretical and Applied Genetics 108: 154-159.
35. Paetkau D, Calvert W, Stirling I, Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4: 347-354.
36. Page RDM. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.
37. Pessoa-Filho M, Beló A, Alcochete AAN, Rangel PHN, Ferreira ME. 2007. A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions. BMC Plant Biology 7: 23.
38. Pillay M, Nwakanma DC, Tenkouano A. 2000. Identification of RAPD markers linked to A and B genome sequences in Musa L. Genome 43: 763-767.
39. Pillay M, Ogundiwin E, Nwakanma DC, Ude G, Tenkouano A. 2001. Analysis of genetic diversity and relationships in East African banana germplasm. Theoretical and Applied Genetics 102: 965-970.
40. Pompanon F, Bonin A, Bellemain E, Taberlet P. 2005. Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics 6: 847-859.
41. Risterucci AM, Hippolyte I, Perrier X, Xia L, Caig V, Evers M, Huttner E, Kilian A, Glaszmann JC. 2009. Development and asssesment of Diversity Arrays Technology for high-throughput DNA analyses in Musa. Theoretical and Applied Genetics 119: 1093-1103.
42. Röder MS, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke RJ, Vosman B, Ganal M. 2002. Construction and analysis of a microsatellite-based database of European wheat varieties. Theoretical and Applied Genetics 106: 67-73.
43. Roux N, Toloza A, Radecki Z, Zapata-Arias FJ, Doležel J. 2003. Rapid detection of aneuploidy in Musa using flow cytometry. Plant Cell Reports 21: 483-490.
44. Ruangsuttapha S, Eimert K, Schröder MB, Silayoi B, Denduangboripant J, Kanchanapoom K. 2007. Molecular phylogeny of banana cultivars from Thailand based on HAT-RAPD markers. Genetic Resources and Crop Evolution 54: 1565-1572.
45. Schuelke M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233-234.
46. SimmondsNW, Shepherd K. 1955. Taxonomy and origin of cultivated bananas. Botanical Journal of the Linnean Society 55: 302-312.
47. Stover RH, Simmonds NW. 1987. Bananas, 3rd edn. Burnt Mill, Harlow: Longman Scientific and Technical.
48. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, Waits LP, Bouvet J. 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24: 3189-3194.
49. Testolin R, Marrazzo T, Cipriani G, Quarta R, Verde I, Dettori MT, Pancaldi M, Sansavini S. 2000. Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43: 512-520.
50. This P, Jung A, Boccaccii P, Borrego J, Botta R, Constantini L, Crespan M, Dangl GS, Eisenheld C, Ferreira-Monteiro F, Grando S, Ibanẽz J, Lacombe T, Laucou V, Magalhaẽs R, Meredith CP, Milani N, Peterlung E, Regner F, Zulini L, Maul E. 2004. Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theoretical and Applied Genetics 109: 1448-1458.
51. Ude G, Pillay M, Nwakanma D, Tenkouano A. 2002. Genetic diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP markers. Theoretical and Applied Genetics 104: 1246-1252.
52. Van Treuren R, Kemp H, Ernsting G, Jongejans B, Houtman H, Visser L. 2010. Microsatellite genotyping of apple (Malus x domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genetic Resources and Crop Evolution 57: 853-865.
53. Venkatachalam L, Sreedhar RV, Bhagyalakshmi N. 2008. The use of genetic markers for detecting DNA polymorphism, genotype identification and phylogenetic relationships among banana cultivars. Molecular Phylogenetics and Evolution 47: 974-985.
54. Virk PS, Newbury HJ, Jackson TM, Ford-Lloyd BV. 1995. The identification of duplicate accessions within a rice germplasm collection using RAPD analysis. Theoretical and Applied Genetics 90: 1049-1055.
55. Wagner HW, Sefc KM. 1999. IDENTITY 1.0. Vienna: Centre for Applied Genetics, University of Agricultural Sciences.
56. Wang JY, Zheng LS, Huang BZ, Liu WL, Wu YT. 2010. Development, characterization and variability analysis of microsatellites from a commercial cultivar of Musa acuminata. Genetic Resources and Crop Evolution 57: 553-563.
57. Wang XL, Chiang TY, Roux N, Hao G, Ge XJ. 2007. Genetic diversity of wild banana (Musa balbisiana Colla) in China as revealed by AFLP markers. Genetic Resources and Crop Evolution 54: 1125-1132.
58. Website 1. Global Musa Genomics Consortium. http://www.musagenomics.org/cetest_firstpage1/genomic_dna.html (28 January 2011).
59. Weeks DE, Conley YP, Ferrell RE, Mah TS, Gorin MB. 2002. A tale of two genotypes: consistency between two high-throughput genotyping centers. Genome Research 12: 430-435.
60. Weising K, Nybom H, Wollf K, Kahl G. 2005. DNA fingerprinting in plants. Principles, methods, and applications, 2nd edn. London: Taylor & Francis.
61. Wong C, Kiew R, Loh JP, Gan LH, Set O, Lee SK, Lum S, Gan YY. 2001a. Genetic diversity of the wild banana Musa acuminata Colla in Malaysia as evidenced by AFLP. Annals of Botany 88: 1017-1025.
62. Wong C, Kiew R, Ohn S, Lamb A, Lee SK, Gan LH, Gan YY. 2001b. Sectional placement of three Bornean species of Musa (Musaceae) based on AFLP. Gardens' Bulletin Singapore 53: 327-341.
63. Wong C, Kiew R, Argent G, Set O, Lee SK, Gan YY. 2002. Assessment of the validity of the sections in Musa (Musaceae) using AFLP. Annals of Botany 90: 231-238.
64. Zhang D, Mischke S, Goenaga R, Hemeida AA, Saunders JA. 2006. Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Science 46: 2084-2092.