The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints

Annals of Botany

Volumn 95, Issue 1, 2005, Pages 237-246

  Fay, Michael F ^a   Cowan, Robyn S ^a   Leitch, Ilia J ^a  

^a ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

AFLP; C value; Genome size; Ploidy; Repetitive DNA

Indexed keywords

ANGIOSPERM; DNA; GENOME; PLOIDY;

ALISMA; BIXA ORELLANA; DAMASONIUM ALISMA; MAGNOLIOPHYTA;

PLANT DNA;

ANGIOSPERM; ARTICLE; CELL NUCLEUS; DNA FINGERPRINTING; GENETIC SELECTION; GENETICS; GENOME; METHODOLOGY; PLOIDY; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SPECIES DIFFERENCE;

ANGIOSPERMS; CELL NUCLEUS; DNA FINGERPRINTING; DNA, PLANT; GENOME, PLANT; PLOIDIES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; SELECTION (GENETICS); SPECIES SPECIFICITY;

EID: 21644466853     PISSN: 03057364     EISSN: None     Source Type: Journal    
DOI: 10.1093/aob/mci017     Document Type: Conference Paper

References (64)

1. Alonso-Blanco C, Peeters AJM, Koornneef M, Lister C, Dean C, van den Bosch N, Pot J, Kuiper MTR. 1998. Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant Journal 14: 259-271.
2. Applied Biosystems. 1996. AFLP plant mapping protocol. Part Number 4303146C. Foster City, CA: Applied Biosystems.
3. Bennett MD, Bhandol P, Leitch IJ. 2000. Nuclear DNA amounts in angiosperms and their modern uses - 807 new estimates. Annals of Botany 86: 859-909.
4. Bennett MD, Leitch IJ. 1995. Nuclear DNA amounts in angiosperms. Annals of Botany 76: 113-176.
5. Bennett MD, Leitch IJ. 2003. Plant DNA C-values database. Release 2.0. http://www.rbgkew.org.uk/cval/homepage.html.
6. Bennett MD, Leitch IJ, Hanson L. 1998. DNA amounts in two samples of weeds. Annals of Botany 82 (suppl. A): 121-134.
7. Bennett MD, Leitch IJ, Price HJ, Johnston JS. 2003. Comparisons with Caenorhabditis (∼100 Mb) and Drosophila (∼175 Mb) using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25 % larger than the Arabidopsis Genome Initiative estimate of ∼125 Mb. Annals of Botany 91: 547-557.
8. Bennett MD, Smith JB. 1976. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 274: 227-274.
9. Bennetzen J. 2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36.
10. Bennetzen J, Ma J, Devos KM. 2005. Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95: 127-132.
11. Brysting AK, Fay MF, Leitch IJ, Aiken SG. 2004. One or more species in the arctic grass genus Dupontia? - A contribution to the Panarctic Flora project. Taxon 53: 365-382.
12. Brzosko E, Ratkiewicz M, Wróblewska A. 2002. Allozyme differentiation and genetic structure of the lady's slipper (Cypripedium calceolus) island populations in north-east Poland. Botanical Journal of the Linnean Society 138: 433-440.
13. Brzosko E, Wróblewska A. 2003. Genetic variation and clonal diversity in island Cephalanthera rubra populations from the Biebrza National Park, Poland. Botanical Journal of the Linnean Society 143: 99-108.
14. Chen X, Boon LS, Man Wong S, Hwa Lee Y, Kuo J, Wing Yam T, Lin JJ. 1999. Amplified fragment length polymorphism analysis in vandaceous orchids. Plant Science 141: 183-189.
15. Costa P, Pot D, Dubos C, Frigerio JM, Pion C, Bodenes C, Bertocchi E, Cervera M-T, Remington DL, Plomion C. 2000. A genetic map of maritime pine based on AFLP, RAPD and protein markers. Theoretical and Applied Genetics 100: 39-48.
16. Dickson EE, Arumuganathan K, Kresovich S, Doyle JJ. 1992. Nuclear DNA content variation within the Rosaceae. American Journal of Botany 79: 1081-1086.
17. Donini P, Elias ML, Bougourd SM, Koebner RMD. 1997. AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs. Genome 40: 521-526.
18. Fay MF, Cowan RS. 2001. Plastid microsatellites in Cypripedium calceolus (Orchidaceae): genetic fingerprints from herbarium specimens. Lindleyana 16: 151-156.
19. Fay MF, Cowan RS, Beltran G, Allen B. 2000. Genetic fingerprinting of two endemics from the Seychelles - Medusagyne oppositifolia (Medusagynaceae) and Rothmannia annae (Rubiaceae). Phelsuma 8: 11-22.
20. Fay MF, Cowan RS, Simpson DA. 2003. Hybridisation between Schoenoplectus tabernaemontani and S. triqueter (Cyperaceae) species in the British Isles. Watsonia 24: 433-442.
21. Fay MF, Gernandt DS, Cowan RS, Kitchen MAR, Kitchen C, Rich TCG. 2002a. Parentage of an unknown member of the Sorbus latifolia (Lam.) Pers. group. Watsonia 24: 91-100.
22. Fay MF, Krauss SL. 2003. Orchid conservation genetics in the molecular age. In: Dixon KW, Kell SP, Barrett RL, Cribb PJ, eds. Orchid conservation. Kota Kinabalu: Natural History Publications (Borneo), 91-112.
23. Fay MF, Lledó MD, Kornblum MM, Crespo MB. 1999. From the waters of Babylon? Populus euphratica in Spain is clonal and probably introduced. Biodiversity and Conservation 8: 769-778.
24. Fay MF, Qamaruz-Zaman F, Cowan RS, Thornton H. 2002b. Molecular techniques for orchid conservation genetic studies. In: J. Clark, Elliott WM, Tingley G, Biro J, eds. Proceedings of the 16th World Orchid Conference. Vancouver: Vancouver Orchid Society, 152-157.
25. Garner TWJ. 2002. Genome size and microsatellites: the effect of nuclear size on amplification potential. Genome 45: 212-215.
26. Goldman DH, Jansen RK, van den Berg C, Leitch IJ, Fay MF, Chase MW. 2004. Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation. American Journal of Botany 91: 707-723.
27. Han T-H, De Jeu M, Van Eck H, Jacobsen E. 2000. Genetic diversity of Chilean and Brazilian Alstroemeria species assessed by AFLP analysis. Heredity 84: 564-569.
28. Han T-H, van Eck HJ, De Jeu MJ, Jacobsen E. 1999. Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp. Theoretical and Applied Genetics 98: 465-471.
29. Hanson L, Brown RL, Boyd A, Johnson MAT, Bennett MD. 2003. First nuclear DNA C-values for 28 angiosperm genera. Annals of Botany 91: 31-38.
30. Hanson L, McMahon KA, Johnson MAT, Bennett MD. 2001. First nuclear DNA C-values for another 25 angiosperm families. Annals of Botany 88: 851-858.
31. Hedrén M, Fay MF, Chase MW. 2001. Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidceae). American Journal of Botany 88: 1868-1880.
32. Hodkinson TR, Chase MW, Renvoize SA. 2002. Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR. Annals of Botany 89: 627-636.
33. Inocencio C, Cowan RS, Alcaraz F, Rivera D, Fay MF. in press. AFLP fingerprinting in Capparis subgenus Capparis related to the commercial sources of capers. Genetic Resources & Crop Evolution.
34. Kentner EK, Arnold ML, Wessler SR. 2003. Characterization of high-copy-number retrotransposons from the large genomes of the Louisiana iris species and their use as molecular markers. Genetics 164: 685-697.
35. Koebner RMD, Powell W, Donini P. 2001. Contributions of DNA molecular marker technologies to the genetics and breeding of wheat and barley. In: Janick J, ed. Plant breeding reviews, 21. Hoboken: John Wiley and Sons, Inc., 181-220.
36. Krauss SL. 1999. Complete exclusion of non-sires in an analysis of paternity in a natural plant population using AFLP. Molecular Ecology 8: 217-226.
37. Krauss SL. 2000. Patterns of mating in Persoonia mollis (Proteaceae) revealed by an analysis of paternity using AFLP: implications for conservation. Australian Journal of Botany 48: 349-356.
38. Krauss SL, Dixon B, Dixon KW. 2002. Rapid genetic decline in a translocated population of the rare and endangered Grevillea scapigera (Proteaceae). Conservation Biology 16: 986-984.
39. Leeton PRJ, Smyth DR. 1993. An abundant LINE-like element amplified in the genome of Lilium speciosum. Molecular and General Genetics 237: 97-104.
40. Leitch IJ, Bennett MD. 2004. Genome downsizing in polyploid plants. Biological Journal of the Linnean Society 82: 651-663.
41. Leitch IJ, Chase MW, Bennett MD. 1998. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Annals of Botany 82: 85-94.
42. Leitch IJ, Soltis DE, Soltis PS, Bennett MD. 2005. Evolution of DNA amounts across land plants (Embryophyta). Annals of Botany 95: 207-217.
43. Maheshwaran M, Subudhi PK, Nandi S, Xu JC, Parco A, Yang DC, Huang N. 1997. Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theoretical and Applied Genetics 94: 39-45.
44. Maunder M, Cowan RS, Stranc P, Fay MF. 2001. The genetic status and conservation management of two cultivated bulb species extinct in the wild: Tecophilaea cyanocrocus (Chile) and Tulipa sprengeri (Turkey). Conservation Genetics 2: 193-201.
45. Micheneau C. 2002. Relations phylogénétiques des Neottieae (Orchidaceae) et étude de la variabilité génétique de Cephalanthera longifolia a l'aide de marqueurs moléculaires (séquencage et microsatellites chloroplastiques). Paris: DEA de Systématique Animale et Végétale, Muséum d'Histoire Naturelle, Paris, France.
46. Mueller UG, Wolfenbarger LL. 1999. AFLP genotyping and fingerprinting. Trends in Ecology and Evolution 14: 389-394.
47. Paglia G, Morgante M. 1998. PCR-based multiplex DNA fingerprinting techniques for the analysis of conifer genomes. Molecular Breeding 4: 173-177.
48. Petrov DA. 2001. Evolution of genome size: new approaches to an old problem. Trends in Genetics 17: 23-28.
49. Petrov DA. 2002. Mutational equilibrium model of genome size evolution. Theoretical Population Biology 61: 531-544.
50. Reamon-Büttner SM, Schmidt T, Jung C. 1999. AFLPs represent repetitive sequences in Asparagus officinalis L. Chromosome Research 7: 297-304.
51. Remington DL, Whetten RW, Liu B-H, O'Malley DM. 1999. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theoretical and Applied Genetics 98: 1279-1292.
52. Richardson JE, Fay MF, Cronk QCB, Chase MW. 2003. Species delimitation and the origin of populations in island representatives of Phylica (Rhamnaceae). Evolution 57: 816-827.
53. Ridout CJ, Donini P. 1999. Use of AFLP in cereals research. Trends in Plant Science 4: 76-79.
54. SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
55. Scacchi R, De Angelis G, Corbo RM. 1991. Effect of breeding system of the genetic structure in three Cephalanthera spp. (Orchidaceae). Plant Systematics and Evolution 176: 53-61.
56. Smyth DR, Kalitsis P, Joseph JL, Sentry JW. 1989. Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila. Proceedings of the National Academy of Science, USA 86: 5015-5019.
57. Solus DE, Soltis PS, Bennett MD, Leitch IJ. 2003. Evolution of genome size in the angiosperms. American Journal of Botany 90: 1596-1603.
58. Travis SE, Maschinski J, Keim P. 1996. An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers. Molecular Ecology 5: 735-745.
59. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I. 2002. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology 11: 139-151.
60. Vinogradov AE. 2003. Selfish DNA is maladaptive: evidence from the plant Red List. Trends in Genetics 19: 609-614.
61. Vos P, Hogers R, Bleeker M, Rijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-4414.
62. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M. 1999. Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theoretical and Applied Genetics 99: 921-935.
63. Wilkinson T, Wetten A, Prychid C, Fay MF. 2003. Suitability of cryopreservation for the long term storage of rare and endangered plant species - a case history for Cosmos atrosanguineus. Annals of Botany 91: 65-74.
64. Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ. 1998. AFLP markers for the study of rice biodiversity. Theoretical and Applied Genetics 96: 602-611.