A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring pinot noir bacterial artificial chromosome contigs

Genetics

Volumn 176, Issue 4, 2007, Pages 2637-2650

  Troggio, Michela ^a   Malacarne, Giulia ^a   Coppola, Giuseppina ^a   Segala, Cinzia ^a   Cartwright, Dustin A ^b   Pindo, Massimo ^a   Stefanini, Marco ^a   Mank, Rolf ^c   Moroldo, Marco ^d,e   Morgante, Michele ^d   Grando, M Stella ^a   Velasco, Riccardo ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b Myriad Genetic Laboratories   (United States)

^c KEYGENE N V   (Netherlands)

^d UNIVERSITY OF UDINE   (Italy)

^e INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; CONTROLLED STUDY; CULTIVAR; GENE MAPPING; GENE SEGREGATION; GENETIC LINKAGE; GENOMICS; GRAPE; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONTIG MAPPING; GENETIC MARKERS; GENOME, PLANT; POLYMORPHISM, SINGLE NUCLEOTIDE; VITIS;

BACTERIA (MICROORGANISMS); VITIS; VITIS VINIFERA;

EID: 34548455424     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.067462     Document Type: Article

References (73)

1. ADAM-BLONDON, A.-F., C. ROUX, D. CLAUX, G. BUTTERLIN, D. MERDINOGLU et al., 2004 Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor. Appl. Genet. 109: 1017-1027.
2. ADAM-BLONDON, A.-F., A. BERNOLE, G. FAES, D. LAMOUREUX, S. PATEYRON et al., 2005 Construction and characterization of BAC libraries from major grapevine cultivars. Theor. Appl. Genet. 110: 1363-1371.
3. ALONSO-BLANCO, C., A. J. M. PEETERS, M. KOORNNEEF, C. LISTER, C. DEAN et al., 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 J. 14: 259-271.
4. ARADHYA, M. K., G. S. DANGL, B. H. PRINS, J. M. BOURSIQUOT, M. A. WALKER et al., 2003 Genetic structure and differentiation in cultivated grape, Vitis vinifera L. Genet. Res. 81: 179-192.
5. BARILLOT, E., B. LACROIX and D. COHEN, 1991 Theoretical analysis of library screening using a N-dimensional pooling strategy. Nucleic Acids Res. 19: 6241-6247.
6. BARKER, C. L., T. DONALD, J. PAUQUET, M. B. RATNAPARKHE, A. BOUQUET et al., 2005 Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor. Appl. Genet. 111: 370-377.
7. BOWERS, J. E., G. S. DANGL, R. VIGNANI and C. P. MEREDITH, 1996 Isolation and characterization of the new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.). Genome 45: 1142-1149.
8. BOWERS, J. E., G. S. DANGL and C. P. MEREDITH, 1999 Development and characterization of additional microsatellite DNA markers for grape. Am. J. Enol. Vit. 50: 243-246.
9. CARTWRIGHT, D. A., M. TROGGIO, R. VELASCO and A. GUTIN, 2007 Genetic mapping in the presence of genotyping errors. Genetics 176: 2521-2527.
10. CASTELLARIN, S. D., G. DI GASPERO, R. MARCONI, A. NONIS, E. PETERLUNGER et al., 2006 Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin. BMC Genomics 7: 12.
11. CASTRO, A. J., C. CARAPITO, N. ZORN, C. MAGNE, E. LEIZE et al., 2005 Proteomic analysis of grapevine (Vitis vinifera L.) tissues subjected to herbicide stress. J. Exp. Bot. 56: 2783-2795.
12. CERVERA, M. T., V. STORME, B. IVENS, J. GUSMÃO, B. H. LIU et al., 2001 Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158: 787-809.
13. CHEN, M., G. PRESTING, W. B. BARBAZUK, J. L. GOICOECHEA, B. BLACKMON et al., 2002 An integrated physical and genetic map of the rice genome. Plant Cell 14: 537-545.
14. DA SILVA, F. G., A. IANDOLINO, F. AL-KAYAL, M. C. BOHLMANN, M. A. CUSHMAN et al., 2005 Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139: 574-597.
15. DI GASPERO, G., G. CIPRIANI, A.-F. ADAM-BLONDON and R. TESTOLIN, 2007 Linkage maps of grapevine displaying the chromosomal location of 420 microsatellite markers and 82 markers for R-gene candidates. Theor. Appl. Genet. 114: 1249-1263.
16. DIRLEWANGER, E., E. GRAZIANO, T. JOOBEUR, F. GARRIGA-CALDERÉ, P. COSSON et al., 2004 Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc. Natl. Acad. Sci. USA 101: 9891-9896.
17. DOLIGEZ, A., A. BOUQUET, Y. DANGLOT, F. LAHOGUE, S. RIAZ et al., 2002 Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theor. Appl. Genet. 105: 780-795.
18. DOLIGEZ, A., A.-F. ADAM-BLONDON, G. CIPRIANI, G. DI GASPERO, V. LAUCOU et al., 2006 An integrated SSR map of grapevine based on five different populations. Theor. Appl. Genet. 113: 369-382.
19. DON, R. H., P. T. COX, B. J. WAINWRIGTH, K. BAKER and J. S. MATTICK, 1991 Touchdown PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 19: 4008.
20. DONALD, T. M., F. PELLERONE, A.-F. ADAM-BLONDON, A. BOUQUET, M. R. THOMAS et al., 2002 Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine. Theor. Appl. Genet. 104: 610-618.
21. DOUCLEFF, M., Y. JIN, F. GAO, S. RIAZ, A. F. KRIVANEK et al., 2004 A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor. Appl. Genet. 109: 1178-1187.
22. DOYLE, J. J., and J. L. DOYLE, 1990 Isolation of plant DNA from fresh tissue. Focus Biotech. 12: 13-15.
23. FANIZZA, G., F. LAMAJ, L. COSTANTINI, R. CHAABANE and M. S. GRANDO, 2005 QTL analysis for fruit yield components in table grapes (Vitis vinifera). Theor. Appl. Genet. 111: 658-664.
24. FARIA, M., A. M. BEJA-PEREIRA, A. MARTINS, M. A. FERREIRA and M. E. S. NUNES, 2004 Grapevine clones discriminated using stilbene synthase-chalcone synthase markers. J. Sci. Food Agric. 84: 1186-1192.
25. FISCHER, B., I. SALAKHUTDINOV, M. AKKURT, R. EIBACH, K. J. EDWARDS et al., 2004 Quantitative trait locus analysis of fungal disease resistance factor on a molecular map of grapevine. Theor. Appl. Genet. 108: 501-515.
26. GAAFAR, R. M., U. HOHMANN and C. JUNG, 2005 Bacterial artificial chromosome-derived molecular markers for early bolting in sugar beet. Theor. Appl. Genet. 110: 1027-1037.
27. GRANDO, M. S., D. BELLIN, K. J. EDWARDS, C. POZZI, M. STEFANINI et al., 2003 Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx. Theor. Appl. Genet. 106: 1213-1224.
28. GRATTAPAGLIA, D., and R. SEDEROFF, 1994 Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 4: 1121-1137.
29. HARALD, H., H. GORING and J. D. TERWILLIGER, 2000 Linkage analysis in the presence of errors II: marker-locus genotyping errors modeled with hypercomplex recombination fractions. Am. J. Hum. Genet. 66: 1107-1118.
30. HORN, R., A.-C. LECOULS, A. CALLAHAN, A. DANDEKAR, L. GARAY et al., 2005 Candidate gene database and transcript map for peach, a model species for fruit trees. Theor. Appl. Genet. 110: 1419-1428.
31. JANSEN, R. C., 1993 Maximum likelihood in a generalized linear finite mixture model by using the EM algorithm. Biometrics 49: 227-231.
32. KEIM, P., J. M. SCHUPP, S. E. TRAVIS, K. CLAYTON, T. ZHU et al., 1997 A high-density soybean genetic map based on AFLP markers. Crop Sci. 37: 537-543.
33. KING, J., I. P. ARMSTEAD, I. S. DONNISON, H. M. THOMAS, R. N. JONES et al., 2002 Physical and genetic mapping in the grasses Lolium perenne and Festuca pratensis. Genetics 161: 315-324.
34. KLEIN, P. E., R. R. KLEIN, S. W. CARTINHOUR, P. E. ULANCH, J. DONG et al., 2000 A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genet. Res. 10: 789-807.
35. KOSAMBI, D. D., 1944 The estimation of map distance from recombination values. Ann. Eugen. 12: 172-175.
36. LIEBHARD, R., B. KOLLER, L. GIANFRANCESCHI and C. GESSLER, 2003 Creating a saturated reference map for the apple (Malus x domestica Borkh.) genome. Theor. Appl. Genet. 106: 1497-1508.
37. LODHI, M. A., and B. I. REISCH, 1995 Nuclear DNA content of Vitis species, cultivars and other genera of the Vitaceae. Theor. Appl. Genet. 90: 11-16.
38. LOWE, K. M., and M. A. WALKER, 2006 Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) x Riparia Gloire (Vitis riparia). Theor. Appl. Genet. 112: 1582-1592.
39. LUO, M. C., C. THOMAS, F. M. YOU, J. HSIAO, S. OUYANG et al., 2003 High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389.
40. MA, H., P. H. MOORE, Z. LIU, M. S. KIM, Q. YU et al., 2004 High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166: 419-436.
41. MERDINOGLU, D., G. BUTTERLIN, L. BEVILACQUA, V. CHIQUET, A.-F. ADAM-BLONDON et al., 2005 Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR. Mol. Breed. 15: 349-366.
42. MICHAELS, S. D., and R. M. AMASINO, 1998 A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J. 14: 381-385.
43. MORGANTE, M., and F. SALAMINI, 2003 From plant genomics to breeding practice. Curr. Opin. Biotechnol. 14: 214-219.
44. MOSER, C., C. SEGALA, P. FONTANA, I. SALAKHUDTINOV, P. GATTO et al., 2005 Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L. Funct. Integr. Genomics 5: 208-217.
45. NEFF, M. M., and E. T. M. KALISHMAN, 2002 Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 18: 613-615.
46. NELSON, W. M., A. K. BHARTI, E. BUTLER, F. WEI, G. FUKS et al., 2005 Whole-genome validation of high-information-content fingerprinting. Plant Physiol. 139: 27-38.
47. ORITA, M., H. IWAHANA, H. KANAZANA, K HAYASHI and T. SEKIYA, 1989 Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2766-2770.
48. PAPA, R., M. TROGGIO, P. AJMONE-M ARSAN and F. NONNIS MARZANO, 2005 An improved protocol for the production of AFLP™ markers in complex genomes by means of capillary electrophoresis. J. Anim. Breed. Genet. 122: 62-68.
49. 1H NMR and chemometrics to characterize mature grape berries in four wine-growing areas in Bordeaux, France. J. Agric. Food Chem. 53: 6382-6389.
50. RAFALSKI, A., 2002 Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94-100.
51. RIAZ, S., G. S. DANGL, K. J. EDWARDS and C. J. MEREDITH, 2004 A microsatellite marker based framework linkage map of Vitis vinifera L. Theor. Appl. Genet. 108: 864-872.
52. SALMASO, M., G. FAES, C. SEGALA, M. STEFANINI, I. SALAKHUTDINOV et al., 2004 Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms. Mol. Breed. 14: 385-395.
53. SARRY, J.-M., N. SOMMERER, F.-X. SAUVAGE, A. BERGOIN, M. ROSSIGNOL et al., 2004 Grape berry biochemistry revisited upon proteomic analysis of the mesocarp. Proteomics 4: 201-215.
54. SCOTT, K. D., P. EGGLER, G. SEATON, M. ROSSETTO, E. M. ABLETT et al., 2000 Analysis of SSR derived from grape ESTs. Theor. Appl. Genet. 100: 723-726.
55. SEFC, K. M., F. REGNER, E. TURETSCHEK, J. GLÖSSL and H. STEINKELLNER, 1999 Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42: 367-373.
56. STADEN, R., K. F. BEAL and J. K. BONFIELD, 2000 The Staden package, 1998. Methods Mol. Biol. 132: 115-130.
57. TANKSLEY, S. D., M. W. GANAL, J. P. PRINCE, M. C. DE VICENTE, M. W. BONIERBALE et al., 1992 High density molecular linkage maps of tomato and potato genomes. Genetics 132: 1141-1160.
58. TERRIER, N., D. GLISSANT, J. GRIMPLET, F. BARRIEU, P. ABBAL et al., 2005 Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development. Planta 222: 832-847.
59. TESTOLIN, R., W. G. HUANG, O. LAIN, R. MESSINA, A. SECCHIONE et al., 2001 A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theor. Appl. Genet. 103: 30-36.
60. THIS, P., A. JUNG, P. BOCCACCI, J. BORREGO, R. BOTTA et al., 2004 Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor. Appl. Genet. 109: 1448-1458.
61. THOMAS, M. R., and N. S. SCOTT, 1993 Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor. Appl. Genet. 86: 985-991.
62. TROGGIO, M., G. MALACARNE, S. VEZZULLI, G. FAES, M. SALMASO et al., 2007 Comparison of different methods for SNP detection in grapevine. Vitis (in press).
63. VAN OS, H. V., S. ANDRZEJEWSKI, E. BAKKER, I. BARRENA, G. BRYAN et al., 2006 Construction of a 10,000 marker ultra-dense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173: 1075-1087.
64. VOORRIPS, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
65. VOS, P., R. HOGERS, M. BLEEKER, M. REIJANS, T. VAN DE LEE et al., 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
66. VOUILLAMOZ, J. F., and M. S. GRANDO, 2006 Genealogy of wine grape cultivars: 'Pinot' is related to Syrah. Heredity 97: 102-110.
67. VUYLSTEKE, M., R. MANK, R. ANTONISE, E. BASTIAANS, M. L. SENIOR et al., 1999 Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor. Appl. Genet. 99: 921-935.
68. WALSH, P. S., H. A. ERLICH and R. HIGUCHI, 1992 Preferential PCR amplification of alleles: mechanisms and solutions. Genome Res. 1: 241-250.
69. WATERS, D. L., T. A. HOLTON, E. M. ABLETT, L. S. LEE and R. J. HENRY, 2005 cDNA microarray analysis of developing grape (Vitis vinifera cv. Shiraz) berry skin. Funct. Integr. Genomics 5: 40-58.
70. YAN, Z., C. DENNEBOOM, A. HATTENDORF, O. DOLSTRA, T. DEBENER et al., 2005 Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor. Appl. Genet. 110: 766-777.
71. YIN, T. M., S. P. DIFAZIO, L. E. GUNTER, D. RIEMENSCHNEIDER and G. A. TUSKAN, 2004 Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor. Appl. Genet. 109: 451-463.
72. YOUNG, W. P., J. M. SCHUPP and P. KEIM, 1999 DNA methylation and AFLP marker distribution in the soybean genome. Theor. Appl. Genet. 99: 785-792.
73. ZHU, Y. L., Q. J. SONG, D. L. HYTEN, C. P. VAN TASSEL, L. K. MATUKUMALLI et al., 2003 Single-nucleotidepolymorphisms insoybean. Genetics 168: 123-1134.