Characterization of sequence polymorphisms from microsatellite flanking regions in Vitis spp

Molecular Breeding

Volumn 22, Issue 3, 2008, Pages 455-465

  Fernandez M P ^a   Nunez Y ^b,c   Ponz, F ^b   Hernaiz S ^a   Gallego, F J ^d   Ibanez J ^a  

^a IMIDRA Finca El Encin   (Spain)

^b ETSI MontesTechnical University of Madrid   (Spain)

^c CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^d UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

DNA markers; Grapevine; Single base extension; Single nucleotide polymorphism; SSR

Indexed keywords

DNA SEQUENCES; GENES; NUCLEOTIDES;

DNA MARKERS; FLANKING REGIONS; GENETIC VARIATION; GRAPEVINE; MICROSATELLITES; SINGLE NUCLEOTIDE POLYMORPHISMS; SINGLE-BASE EXTENSIONS; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS; SSR; VITIS SPP;

CAPILLARY ELECTROPHORESIS;

ANIMALIA; VITACEAE; VITIS; VITIS VINIFERA;

EID: 50249130717     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-008-9189-z     Document Type: Article

References (43)

1. G Ablett H Hill RJ Henry 2006 Sequence polymorphism discovery in wheat microsatellite flanking regions using pyrophosphate sequencing Mol Breed 17 281 289
2. C Arnold M Rossetto J McNally RJ Henry 2002 The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae Am J Bot 89 1 22 28
3. Bhattramakki D, Rafalski A (2001) Discovery and application of single nucleotide polymorphism markers in plants. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI publishing, Lismore
4. SM Blankenship B May D Hedgecock 2002 Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence Mol Biol Evol 19 11 1943 1951
5. JE Bowers GS Dangl R Vignani CP Meredith 1996 Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.) Genome 39 628 633
6. JE Bowers GS Dangl CP Meredith 1999 Development and characterization of additional microsatellite DNA markers for grape Am J Enol Vitic 50 3 243 246
7. J Brohede H Ellengren 1999 Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences Proc R Soc Lond 226 825 833
8. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. Avaible via DIALOG. http://www. biomedcentral.com/1471-2156/3/19
9. De Andrés MT (2001) Caracterización de portainjertos de vid mediante marcadores moleculares. Ph D Dissertation, Universidad de Alcalá de Henares, Madrid
10. JR Dettman JW Taylor 2004 Mutation and evolution of microsatellite loci in Neurospora Genetics 168 1231 1248
11. G Di Gaspero E Peterlunger R Testolin KJ Edwards G Cipriani 2000 Conservation of microsatellite loci within the genus Vitis Theor Appl Genet 101 301 308
12. Edwards KJ, Mogg R (2001) Plant genotyping by analysis of single nucleotide polymorphisms. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI Publishing, Lismore
13. MC Grimaldi B Crouau-Roy 1997 Microsatellite allelic homoplasy due to variable flanking sequences J Mol Evol 44 336 340
14. MP Heaton GP Harhay FL Bennett RT Stone WM Grosse E Casas JW Keele PL Smith CG Ghitko-McKown WW Laegreid 2002 Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle Mamm Genome 13 272 281
15. J Ibáñez MT de Andrés J Borrego 2000 Allelic variation observed at one microsatellite locus between the two synonym grape cultivars Black Currant and Mavri Corinthiaki Vitis 39 4 173 174
16. J Ibáñez MT de Andrés A Molino J Borrego 2003 Genetic study of key Spanish Grapevine varieties using microsatellite analysis Am J Enol Vitic 54 1 22 30
17. O Jaillon JM Aury B Noel A Policriti C Clepet A Casagrande N Choisne A Aubourg N Vitulo C Jubin A Vezzi F Legeai CD Hugueney D Horner E Mica D Jublot J Poulain C Bruyère A Billault B Segurens M Gouyvenoux E Ugarte F Cattonaro V Anthouard V Vico C Del Fabbro M Alaux G Di Gaspero V Dumas N Felice S Paillard I Juman M Moroldo S Scalabrin A Canaguier I Le Clainche G Malacrida E Durand G Pesole V Laucou P Chatelet D Merdinoglu M Delledonne M Pezzotti A Lecharny C Scarpelli F Artiguenave ME Pè G Valle M Morgante M Caboche AF Adam-Blondon J Weissenbach F Quétier P Wincker 2007 The grapevine genome sequence suggests ancestral haxaploidization in major angiosperm phyla Nature 449 7161 463 467
18. MA Jobling P Gill 2004 Encoded evidence: DNA in forensic analysis Nat Rev Genet 5 10 739 751
19. ES Jones H Sullivan D Bhattramakki JSC Smith 2007 A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize Theor Appl Genet 115 361 371
20. R Kota S Rudd A Facius G Kolesov T Thiel H Zhang N Stein K Mayer A Graner 2003 Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.) Mol Genet Genomics 270 24 33
21. Lijavetzky D, Cabezas JA, Ibáñez A, Rodríguez V, Martínez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. Dig BMC Genet doi: 10.1186/1471-2164-8-424
22. KD Makova A Nekrutenko RJ Baker 2000 Evolution of microsatellite alleles in four species of mice (Genus Apodemus) J Mol Evol 51 166 172
23. NM Makridakis JKV Reichardt 2001 Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms Biotechniques 31 1374 1380
24. Marshall T (2001) Cervus 2.0 software. University of Edinburgh, UK
25. R Mogg J Batley S Hanley H Edwards H O'Sullivan KJ Edwards 2002 Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms Theor Appl Genet 105 532 543
26. G Ortí DE Pearse JC Avise 1997 Phyllogenetic assessment of length variation at a microsatellite locus Proc Natl Acad Sci 94 10745 10749
27. Park S (2001) Microsatellite toolkit. Animal and Genomics Laboratory, UCD
28. C Phillips M Lareu J Sanchez M Brion B Sobrino N Morling P Schneider D Syndercombe Court A Carracedo 2004 Selecting single nucleotide polymorphisms for forensic applications Int Congr Ser 1261 18 20
29. JA Rafalski 2002 Novel genetic mapping tools in plants: SNPs and LD-based approaches Plant Sci 162 329 333
30. JA Rafalski 2002 Applications of single nucleotide polymorphisms in crop genetics Curr Opin Plant Biol 5 2 94 100
31. M Rossetto J McNally RJ Henry 2002 Evaluating the potential of SSR flanking regions for examining taxonomic relationships in the Vitaceae Theor Appl Genet 104 61 66
32. S Rudd H Schoof K Mayer 2005 PlantMarkers-a database of predicted molecular markers from plants Nucleic Acids Res 33 D628 D632 10.1093/nar/gki074
33. J Russell A Booth J Fuller B Harrower P Hedley G Machray W Powell 2004 A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome Genome 47 389 398
34. M Salmaso G Faes C Segala M Stefanini I Salakhutdinov E Zyprian R Toepfer MS Grando R Velasco 2004 Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms Mol Breed 14 385 395
35. KM Sefc F Regner E Turetschek J Glössl H Steinkellner 1999 Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species Genome 42 367 373
36. DJ Somers R Kirkpatrick M Moniwa A Walsh 2003 Mining single-nucleotide polymorphisms from hexploid wheat ESTs Genome 49 431 437
37. AC Syvänen 1999 From gels to chips: "Minisequencing" Primer extension for analysis of point mutations and single nucleotide polymorphisms Hum Mutat 13 1 10
38. AC Syvänen 2001 Accessing genetic variation: genotyping single nucleotide polymorphisms Nat Rev Genet 2 930 942
39. MR Thomas NS Scott 1993 Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs) Theor Appl Genet 86 985 990
40. MR Thomas P Cain NS Scott 1994 DNA typing of grapevines: a universal methodology and database for describing cultivars and evaluating genetic relatedness Plant Mol Biol 25 939 949
41. R Velasco A Zharkikh M Troggio DA Cartwright A Cestaro D Pruss M Pindo LM FitzGerald S Vezzulli J Reid G Malacarne D Iliev G Coppola B Wardell D Micheletti T Macalma M Facci JT Mitchell M Perzzolli G Eldredge P Gatto R Oyzerski M Moretto N Gutin M Stefanini Y Chen C Segala C Davenport L Demattè A Mraz J Battilana K Stormo F Costa Q Tao A Si-Ammour T Harkins A Lackey C Perbost B Taillon A Stella V Solovyev JA Fawcett L Sterck K Vandepoele SM Grando S Toppo C Moser J Lanchbury R Bogden M Skolnick V Sgaramella SK Bhatnagar P Fontana A Gutin Y Van de Peer F Salamini R Viola 2007 A high quality draft consensus sequence of the genome of a heterozygous grapevine variety PLoS ONE 2 12 e1326 10.1371/journal.pone.0001326
42. Wagner HW, Sefc KM (1999) IDENTITY 1.0. Centre for Applied Genetics, University of Agricultural Sciences, Vienna
43. YL Zhu QJ Song DL Hyten CP Van Tassell LK Matukumalli DR Grimm SM Hyatt EW Fickus ND Young PB Cregan 2003 Single-nucleotide polymorphisms in Soybean Genetics 163 1123 1134