VvGAI1 polymorphisms associate with variation for berry traits in grapevine

Euphytica

Volumn 191, Issue 1, 2013, Pages 85-98

  Vargas, Alba M ^a   Le Cunff, Loïc ^b,c   This, Patrice ^b   Ibáñez, Javier ^a,d   de Andrés, M Teresa ^a  

^a Dept Agroalimentación   (Spain)

^b CEMAGREF   (France)

^c MONTPELLIER SUPAGRO   (France)

^d UNIVERSITY OF LA RIOJA   (Spain)

Author keywords

Association analysis; Table grape; Vitis vinifera; VvGAI1

Indexed keywords

VITACEAE; VITIS; VITIS VINIFERA;

EID: 84876721049     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-013-0866-6     Document Type: Article

References (70)

1. Abdurakhmonov IY, Abdukarimov A (2008) Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics 2008: 574-927.
2. Aradhya MK, Dangl GS, Prins BH, Boursiquot JM, Walker MA, Meredith CP, Simon CJ (2003) Genetic structure and differentiation in cultivated grape, Vitis vinifera L. Genet Res 81: 179-192.
3. Arroyo-García R, Ruiz-Garcia L, Bolling L, Ocete R, López MA, Arnold C, Ergul A, Soylemezoglu G, Uzun HI, Cabello F, Ibáñez J, Aradhya MK, Atanassov A, Atanassov I, Balint S, Cenis JL, Costantini L, Goris-Lavets S, Grando MS, Klein BY, McGovern PE, Merdinoglu D, Pejic I, Pelsy F, Primikirios N, Risovannaya V, Roubelakis-Angelakis KA, Snoussi H, Sotiri P, Tamhankar S, This P, Troshin L, Malpica JM, Lefort F, Martínez-Zapater JM (2006) Multiple origins of cultivated grapevine (Vitis vinifera L. ssp sativa) based on chloroplast DNA polymorphisms. Mol Ecol 15: 3707-3714.
4. Battilana J, Costantini L, Emanuelli F, Sevini F, Segala C, Moser S, Velasco R, Versini G, Grando MS (2009) The 1-deoxy-D-xylulose 5-phosphate synthase gene co-localizes with a major QTL aVecting monoterpene content in grapevine. Theor Appl Genet 118: 653-669.
5. Boss PK, Thomas MR (2002) Association of dwarfism and floral induction with a grape 'green revolution' mutation. Nature 416: 847-850.
6. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
7. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46: 1323-1330.
8. Cabezas JA, Cervera MT, Ruiz-Garcia L, Carreno J, Martínez-Zapater JM (2006) A genetic analysis of seed and berry weight in grapevine. Genome 49: 1572-1585.
9. Chaïb J, Torregrosa L, Mackenzie D, Corena P, Bouquet A, Thomas MR (2010) The grape microvine-a model system for rapid forward and reverse genetics of grapevines. Plant J 62(6): 1083-1092.
10. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. doi: 10. 1186/1471-2156-3-19.
11. Chung SM, Staub JE (2003) The development and evaluation of concensus chloroplast SSRs for chloroplast genetic analysis. Theor Appl Genet 107: 757-767.
12. Costantini L, Battilana J, Lamaj F, Fanizza G, Grando MS (2008) Berry and phenology-related traits in grapevine (Vitisvinifera L.): from quantitative trait loci to underlying genes. BMC Plant Biol. doi: 10. 1186/1471-2229-8-38.
13. Cunha J, Teixeira Santos M, Carneiro LC, Fevereiro P, Eiras-Dias JE (2009) Portuguese traditional grapevine cultivars and wild vines (Vitis vinifera L.) share morphological and genetic traits. Genet Resour Crop Ev 56: 975-989.
14. Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C, Schooley DA, Schlauch KA, Cushman JC, Cramer GR (2007) Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genomics. doi: 10. 1186/1471-2164-8-429.
15. Doligez A, Bouquet A, Danglot Y, Lahogue F, Riaz S, Meredith CP, Edwards KJ, This P (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.
16. Doligez A, Bertrand Y, Dias S, Grolier M, Ballester JF, Bouquet A, This P (2010) QTLs for fertility in table grape. Tree Genet Genomes 6(3): 413-422.
17. Emanuelli F, Battilana J, Costantini L, Le Cunff L, Boursiquot JM, This P, Grando MS (2010) A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.). BMC Plant Biol. doi: 10. 1186/1471-2229-10-241.
18. Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequilibrium and association mapping in crop plants. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement: vol. 1 genomics approaches and platforms. Springer, The Netherlands, pp 97-119.
19. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14: 2611-2620.
20. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
21. Fanizza G, Lamaj F, Costantini L, Chaabane R, Grando MS (2005) QTL analysis for fruit yield components in table grapes (Vitis vinifera). Theor Appl Genet 111: 658-664.
22. Fournier-Level A, Le Cunff L, Gomez C, Doligez A, Ageorges A, Roux C, Bertrand Y, Souquet JM, Cheynier V, This P (2009) Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study. Genetics 183: 1127-1139.
23. Fournier-Level A, Hugueney P, Verriès C, This P, Ageorges A (2011) Genetic mechanisms underlying the methylation level of anthocyanins in grape (Vitis vinifera L.). BMC Plant Biol. doi: 10. 1186/1471-2229-11-179.
24. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
25. Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB (2008) Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC Plant Biol. doi: 10. 1186/1471-2229-8-7.
26. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: an algorithm for building germ plasm core collections by maximaizing allelic or phenotypic richness. J Hered 92: 93-94.
27. Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC (2007) Tissue-specific mRNA expression profiling in grape berry tissues. BMC Genomics. doi: 10. 1186/1471-2164-8-187.
28. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
29. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
30. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4: 45-61.
31. Houel C, Bounon R, Chaïb J, Guichard C, Péros JP, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A, Le Paslier MC, Vernerey MS, Coriton O, Brunel D, This P, Torregrosa L, Adam-Blondon AF (2010) Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC Plant Biol 10: 284-299.
32. Huang YF, Doligez A, Fournier-Level A, Le Cunff L, Bertrand Y, Canaguier A, Morel C, Miralles V, Veran F, Souquet JM, Cheynier V, Terrier N, This P (2012) Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping. BMC Plant Biol 12: 30-59.
33. Hudson RR (1987) Estimating the recombination parameter of a finite population-model without selection. Genet Res 50: 245-250.
34. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA-sequences. Genetics 111: 147-164.
35. Ibáñez J, Vargas AM, Palancar M, Borrego J, de Andres MT (2009) Genetic relationships among table-grape varieties. Am J Enol Vitic 60: 35-42.
36. Imazio S, Labra M, Grassi F, Scienza A, Failla O (2006) Chloroplast microsatellites to investigate the origin of grapevine. Genet Resour Crop Ev 53: 1003-1011.
37. Karaagac E, Vargas AM, de Andrés MT, Carreño I, Ibánez I, Carreño J, Martínez-Zapater JM, Cabezas JA (2012) Marker assisted selection for seedlessness in table grape breeding. Tree Genet Genomes. doi: 10. 1007/s11295-012-0480-0.
38. Khan MA, Korban SS (2012) Association mapping in forest trees and fruit crops. J Ex Bot. doi: 10. 1093/jxb/ers105.
39. Le Cunff L, Fournier-Level A, Laucou V, Vezzuli S, Lacombe T, Adam-Blondon A, Boursiquot JM, This P (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa. BMC Plant Biol. doi: 10. 1186/1471-2229-8-31.
40. Lijavetzky D, Ruiz-Garcia L, Cabezas JA, De Andrés MT, Bravo G, Ibáñez A, Carreño J, Cabello F, Ibáñez J, Martínez-Zapater JM (2006) Molecular genetics of berry colour variation in table grape. Mol Genet Genomics 276: 427-435.
41. Lijavetzky D, Cabezas JA, Ibáñez A, Rodriguez 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. BMC Genomics. doi: 10. 1186/1471-2164-8-424.
42. Mejía N, Gebauer M, Muñoz L, Hewstone N, Muñoz C, Hinrichsen P (2007) Identification of QTLs for seedlessness, berry size, and ripening date in a seedless x seedless table grape progeny. Am J Enol Vitic 58(4): 499-507.
43. Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, Miccono MA, Ramos R, Le Cunff L, Boursiquot JM, Hinrichsen P, Adam-Blondon AF (2011) Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC Plant Biol. doi: 10. 1186/1471-2229-11-57.
44. Mullins MG, Bouquet A, Williams LE (1992) Biology of grapevine. Cambridge University Press, Cambridge.
45. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
46. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9: 325-330.
47. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
48. Olszewski N, Sun TP, Gubler F (2002) Gibberellin signaling: biosynthesis, catabolism, and response pathways. Plant Cell 14: S61-S80.
49. Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.
50. Pritchard JK, Stephens M, Donnely P (2000a) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
51. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67: 170-181.
52. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doeblay J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. P Natl Acad Sci USA 98: 11479-11484.
53. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
54. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
55. Ruperti B, Bonghi C, Ziliotto F, Pagni S, Rasori A, Varotto S, Tunutti P, Giovannoni JJ, Ramina A (2002) Characterization of a major latex protein (mlp) gene down-regulated by ethylene during peach fruitlet abscission. Plant Sci 163: 265-272.
56. Salmaso M, Faes G, Segala C, Stefanini M, Salakhutdinov L, Zyprian E, Toepfer R, Grando MS, Velasco R (2004) Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms. Mol Breeding 14: 385-395.
57. Sato A, Yamada M, Iwanami H, Mitani N (2004) Quantitative and instrumental measurements of grape flesh texture as affected by gibberellic acid application. J Jpn Soc Hortic Sci 73: 7-11.
58. Sefc KM, Regner F, Turetschek E, Glössl J, Steinkellner H (1999) Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42: 367-373.
59. Singh K, Weaver RJ, Johnson JO (1978) Effect of applications of gibberellic-acid on berry size, shatter, and texture of Thompson seedless grapes. Am J Enol Vitic 29: 258-262.
60. Sorkheh K, Malysheva-Otto LV, Wirthensohn MG, Tarkesh-Esfahani S, Martínez-Gómez P (2008) Linkage disequilibrium, genetic association mapping and gene localization in crop plants. Genet Mol Biol 31: 805-814.
61. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
62. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21: 1214-1225.
63. This P, Lacombe T, Cadle-Davidson M, Owens CL (2007) Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theor Appl Genet 114: 723-730.
64. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286-289.
65. Vargas AM, de Andrés MT, Borrego J, Ibáñez J (2009) Pedigrees of fifty table-grape cultivars. Am J Enol Vitic 60(4): 525-532.
66. Watterson GA (1975) Number of segregating sites in genetic models without recombination. Theor Popul Biol 7: 256-276.
67. Weising K, Gardner RC (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42: 9-19.
68. Wen J, Nie Z-L, Soejima A, Meng Y (2007) Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences. Can J Bot 85: 731-745.
69. Winkler AJ, Cook JA, Kliewer WM, Lider LA (1974) General viticulture. University of California Press, Berkeley.
70. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1: 5-20.