Candidate loci for phenology and fruitfulness contributing to the phenotypic variability observed in grapevine

Theoretical and Applied Genetics

Volumn 126, Issue 11, 2013, Pages 2763-2776

  Grzeskowiak, Lukasz ^a   Costantini, Laura ^a   Lorenzi, Silvia ^a   Grando, M Stella ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELIC VARIATION; CLIMATIC CONDITIONS; FERTILITY VARIATION; FRUIT DEVELOPMENT; GEOGRAPHICAL LOCATIONS; PHENOTYPIC VARIATIONS; PUTATIVE FUNCTIONS; QUANTITATIVE TRAIT LOCUS;

FRUITS; GENES; PLANTS (BOTANY); WINE;

CULTIVATION;

VITACEAE; VITIS; VITIS VINIFERA;

ARTICLE; CHROMOSOME MAP; FERTILITY; FRUIT; GENETIC ASSOCIATION; GENETICS; PHENOTYPE; PHYSIOLOGY; PLANT GENOME; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; VITIS;

CHROMOSOME MAPPING; FERTILITY; FRUIT; GENETIC ASSOCIATION STUDIES; GENOME, PLANT; PHENOTYPE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; VITIS;

EID: 84887609943     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-013-2170-1     Document Type: Article

References (82)

1. Abel S, Savchenko T, Levy M (2005) Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa. BMC Evol Biol 5: 72.
2. Amerine MA, Winkler AJ (1944) Composition and quality of musts and wines of California grapes. Hilgardia 15: 493-675.
3. Anderson JT, Inouye DW, McKinney AM, Colautti RI, Mitchell-Olds T (2012) Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change. Proc R Soc B 279: 3843-3852.
4. Bienert MD, Delannoy M, Navarre C, Boutry M (2012) NtSCP1 from tobacco is an extracellular serine carboxypeptidase III that has an impact on cell elongation. Plant Physiol 158: 1220-1229.
5. Bock A, Sparks T, Estrella N, Menzel A (2011) Changes in the phenology and composition of wine from Franconia, Germany. Clim Res 50(1): 69-81.
6. Bourquin V, Nishikubo N, Abe H, Brumer H, Denman S, Eklund M, Christiernin M, Teeri TT, Sundberg B, Mellerowicz EJ (2002) Xyloglucan endotransglycosylases have a function during the formation of secondary cell walls of vascular tissues. Plant Cell 14: 3073-8308.
7. Braidot E, Zancani M, Petrussa E, Peresson C, Bertolini A, Patui S, Macrì F, Vianello A (2008) Transport and accumulation of flavonoids in grapevine (Vitis vinifera L.). Plant Signal Behav 3(9): 626-632.
8. Brunet M, Jones PD, Sigró J, Saladié O, Aguilar E, Moberg A, Della-Marta PM, Lister D, Walther A, López D (2007) Temporal and spatial temperature variability and change over Spain during 1850-2005. J Geophys Res 112: D12117.
9. Buchanan M, Burton RA, Dhugga KS, Rafalski AJ, Tingey SV, Shirley NJ, Fincher GB (2012) Endo-(1, 4)-β-Glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes. BMC Plant Biol 12(1): 235.
10. Caffarra A, Eccel E (2011) Projecting the impacts of climate change on the phenology of grapevine in a mountain area. Austr J Grape Wine R 17: 52-61.
11. Caillaud MC, Paganelli L, Lecomte P, Deslandes L, Quentin M, Pecrix Y, Le Bris M, Marfaing N, Abad P, Favery B (2009) Spindle assembly checkpoint protein dynamics reveal conserved and unsuspected roles in plant cell division. PLoS ONE 4: e6757.
12. Carmona MJ, Calonje M, Martinez-Zapater JM (2007) The FT/TFL1 gene family in grapevine. Plant Mol Biol 63: 637-650.
13. Carreño Ruiz I (2012) Identificación de regiones cromosómicas implicadas en el control genético de caracteres de interés para la mejora genética de la uva de mesa. Proyecto de investigación, Universidad de Murcia.
14. Carrier G, Huang YF, Le Cunff L, Fournier-Level A, Vialet S, Souquet JM, Cheynier V, Terrier N, This P (2013) Selection of candidate genes for grape proanthocyanidin pathway by an integrative approach. Plant Physiol Biochem. doi: 10. 1016/j. plaphy. 2013. 04. 014.
15. Chew YH, Wilczek AM, Williams M, Welch SM, Schmitt J, Halliday KJ (2012) An augmented Arabidopsis phenology model reveals seasonal temperature control of flowering time. New Phytol 194(3): 654-665.
16. Chuine I, Yiou P, Viovy N, Seguin B, Daux V, Le Roy Ladurie E (2004) Grape ripening as a past climate indicator. Nature 432: 289-290.
17. Clark SE, Williams RW, Meyerowitz EM (1997) The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell 89: 575-585.
18. Coombe BG (1988) Grape phenology. In: Coombe BG, Dry PR (eds) Viticulture, vol 1, Resources. Winetitles, Adelaide, pp 139-153.
19. Coombe BG (1995) Adoption of a system for identifying grapevine growth stages. Aust J Grape Wine Res 1: 104-110.
20. Cosgrove DJ (2000) Loosening of plant cell walls by expansins. Nature 407: 321-326.
21. Costantini L, Battilana J, Lamaj F, Fanizza G, Grando MS (2008) Berry and phenology-related traits in grapevine (Vitis vinifera L.): from quantitative trait loci to underlying genes. BMC Plant Biol 8: 38.
22. Dal Santo S, Tornielli GB, Zenoni S, Fasoli M, Farina L, Anesi A, Guzzo F, Delledonne M, Pezzotti M (2013a) The plasticity of the grapevine berry transcriptome. Genome Biol 14: R54.
23. Dal Santo S, Vannozzi A, Tornielli GB, Fasoli M, Venturini L, Pezzotti M, Zenoni S (2013b) Genome-wide analysis of the expansin gene superfamily reveals grapevine-specific structural and functional characteristics. PLoS ONE 8(4): e62206.
24. Diaz-Riquelme J, Lijavetzky D, Martinez-Zapater JM, Carmona MJ (2009) Genome-wide analysis of MIKCC-type MADS Box genes in grapevine. Plant Physiol 149: 354-369.
25. 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.
26. Dry PR (1983) Recent advances in Australian viticulture. Advances in viticulture and oenology for economic gain. In: Lee TH, Somers TC (eds) Proceedings of Fifth Aust Wine Industry Tech Conference, 29 Nov-1 Dec 1983, Perth, WA, Aust Wine Res Institute, vol 1984, pp 9-23.
27. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70.
28. Duchêne E, Schneider C (2005) Grapevine and climatic changes: a glance at the situation in Alsace. Agron Sustain Dev 25: 93-99.
29. Duchêne E, Huard F, Dumas V, Schneider C, Merdinoglu D (2010) The challenge of adapting grapevine varieties to climate change. Clim Res 41: 193-204.
30. Duchêne E, Butterlin G, Dumas V, Merdinoglu D (2012) Towards the adaptation of grapevine varieties to climate change: QTLs and candidate genes for developmental stages. Theor Appl Genet 124(4): 623-635.
31. Durbak AR, Tax FE (2011) CLAVATA signaling pathway receptors of Arabidopsis regulate cell proliferation in fruit organ formation as well as in meristems. Genetics 189: 177-194.
32. Edwards R, Dixon DP, Walbot V (2000) Plant glutathione S-transferases: enzymes with multiple functions in sickness and in health. Trends Plant Sci 5: 193-198.
33. Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS (2013) Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 13: 39.
34. Fanizza G, Lamaj F, Costantini L, Chaabane R (2005) QTL analysis for fruit yield components in table grapes (Vitis vinifera). Theor Appl Genet 111: 658-664.
35. Forcato C (2010) Gene prediction and functional annotation in the Vitis vinifera genome. In Università Degli Studi Di Padova. PhD Thesis.
36. Fortes AM, Agudelo-Romero P, Silva MS, Ali K, Sousa L, Maltese F, Choi YH, Grimplet J, Martinez-Zapater JM, Verpoorte R, Pais MS (2011) Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening. BMC Plant Biol 11: 149.
37. Fournier-Level A, Lacombe T, Le Cunff L, Boursiquot JM, This P (2010) Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.). Heredity 104(4): 351-362.
38. Fraser CM, Rider LW, Chapple C (2005) An expression and bioinformatics analysis of the Arabidopsis serine carboxypeptidase-like gene family. Plant Physiol 138: 1136-1148.
39. Gambetta GA, Matthews MA, Shaghasi TH, McElrone AJ, Castellarin SD (2010) Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape. Planta 232: 219-234.
40. Ghelardini L, Falusi M, Santini A (2006) Variation in timing of bud-burst of Ulmus minor clones from different geographical origins. Can J Forest Res 36: 1982-1991.
41. Grimplet J, van Hemert J, Carbonell-Bejerano P, Diaz-Riquelme J, Fennell A, Pezzotti M, Martinez-Zapater JM (2012) Comparative analysis of grapevine whole-genome predictions, functional annotation and categorization of the predicted gene sequences. BMC Res notes 5: 213.
42. Hannah L, Roehrdanz PR, Ikegami M, Shepard AV, Shaw MR, Tabor G, Zhi L, Marquet PA, Hijmans RJ (2013) Climate change, wine, and conservation. PNAS. doi: 10. 1073/pnas. 1210127110.
43. Hunter AF, Lechowicz MJ (1992) Predicting the timing of budburst in temperate trees. J Appl Ecol 25: 597-604.
44. Jackson RS (2008) Wine science: principles and applications. Elsevier, San Diego.
45. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quétier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
46. Jones GV, White MA, Cooper OR, Storchmann K (2005) Climate change and global wine quality. Clim Change 73: 319-343.
47. Keller M (2010) Managing grapevines to optimise fruit development in a challenging environment: a climate change primer for viticulturists. Aust J Grape Wine Res 16: 56-69.
48. Kline KG, Sussman MR, Jones AM (2010) Abscisic acid receptors. Plant Physiol 154: 479-482.
49. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304: 982.
50. Kottek M, Grieser J, Beck C, Rudolf B, Rubel F (2006) World map of Koeppen-Geiger climate classification updated. Meteorol Z 15: 259-263.
51. Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, Strack D, Chapple C (2000) Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell 12: 1295-1306.
52. Lehmann E (1975) Nonparametrics. McGraw-Hill, New York.
53. Lieth H (ed) (1974) Phenology and seasonality modelling. Springer, New York.
54. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.
55. Martinez-Zapater JM, Carmona MJ, Diaz-Riquelme J, Fernandez L, Lijavetzky D (2010) Grapevine genetics after the genome sequence: challenges and limitations. Aust J Grape Wine Res 16: 33-46.
56. Morris JR, Main GL (2010) Response of Concord grapevines to varied shoot positioning and pruning methods in a warm, long-season growing region. Am J Enol Vitic 61: 201-213.
57. Motose H, Iwamoto K, Endo S, Demura T, Sakagami Y, Matsubayashi Y, Moore KL, Fukuda H (2009) Involvement of phytosulfokine in the attenuation of stress response during the transdifferentiation of Zinnia mesophyll cells into tracheary elements. Plant Phys 150: 437-447.
58. Nakamura M, Katsumata H, Abe M, Yabe N, Komeda Y, Yamamoto K, Takahashi T (2006) Characterisation of the class IV homeodomain-leucine zipper gene family in Arabidopsis. Plant Physiol 141: 1363-1375.
59. Nicotra AB, Atkin OK, Bonser SP, Davidson A, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M (2010) Plant phenotypic plasticity in a changing climate. Trends Plant Sci 15: 684-692.
60. Nunan KJ, Davies C, Robinson SP, Fincher GB (2001) Expression patterns of cell wall-modifying enzymes during grape berry development. Planta 214: 257-264.
61. Parage C, Tavares R, Rety S, Baltenweck-Guyot R, Poutaraud A, Renault L, Heintz D, Lugan R, Marais G, Aubourg S, Hugueney P (2012) Structural, functional, and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine. Plant Physiol 160: 1407-1419.
62. Sadras VO, Reynolds M, De la Vega AJ, Petrie PR, Robinson R (2009) Phenotypic plasticity of yield and phenology in wheat, sunflower and grapevine. Field Crops Res 110: 242-250.
63. Sánchez LA, Dokoozlian NK (2005) Bud microclimate and fruitfulness in Vitis vinifera L. Am J Enol Vitic 56: 319-329.
64. Sansavini S, Fanigliulo G (1998) Bud fertility and effects of pruning of seedless grapevine varieties Centennial Seedless and Sugraone [Basilicata - Vitis vinifera L.]. Rivista di Frutticoltura e di Ortofloricoltura 60(2): 55-60.
65. Schmitz RJ, Hong L, Michaels S, Amasino RM (2005) FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development 132: 5471-5478.
66. Schnelle F (1955) Pflanzen-Phänologie. Akademische Verlagsgesellschaft, Leipzig.
67. Schultz HR (2000) Climate change and viticulture: a European perspective on climatology, carbon dioxide and UV-B effects. Austr J Grape Wine R 6: 2-12.
68. Schulze S, Schäfer BN, Parizotto EA, Voinnet O, Theres K (2010) LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems. Plant J 64: 668-678.
69. Sommer KJ, Islam MT, Clingeleffer PR (2000) Light and temperature effects on shoot fruitfulness in Vitis vinifera L. cv. Sultana: influence of trellis type and grafting. Austr J Grape Wine R 6: 99-108.
70. Sparks TH, Menzel A (2002) Observed changes in seasons: an overview. Int J Climatol 22: 1715-1725.
71. Tomasi D, Jones GV, Giust M, Lovat L, Gaiotti F (2011) Grapevine phenology and climate change: relationships and trends in the Veneto Region of Italy for 1964-2009. Am J Enol Vitic 62: 329-339.
72. Troggio M, Malacarne G, Coppola G, Segala C, Cartwright DA, Pindo M, Stefanini M, Mank R, Moroldo M, Morgante M, Grando MS, Velasco R (2007) A dense single-nucleotide-polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 176: 2637-2650.
73. Unver T, Parmaksi{dotless}z İ, Dündar E (2010) Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep 29: 757-769.
74. van Leeuwen C, Garnier C, Agut C, Baculat B, Barbeau G, Besnard E, Bois B, Boursiquot JM, Chuine I, Dessup T, Dufourcq T, Garcia-Cortazar I, Marguerit E, Monamy C, Koundouras S, Payan JC, Parker A, Renouf V, Rodriguez-Lovelle B, Roby JP, Tonietto J, Trambouze W (2008) Heat requirements for grapevine varieties is essential information to adapt plant material in a changing climate. In: Proceedings of VIIth International Terroir Congress, 20-23 May, Nyon, Switzerland, vol 1, pp 222-227.
75. van Ooijen JW (2009) MapQTL® 6: Software for the mapping of quantitative trait loci in experimental populations of diploid species. Wageningen, Netherlands, Kyazma BV.
76. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma TM, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Amour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando MS, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, van de Peer Y, Salamini F, Viola R (2007) High quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2: e1326.
77. Wang D, Guo YH, Wu CG, Yang GD, Li YY, Zheng CH (2008) Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics 9: 44.
78. Webb LB, Whetton PH, Barlow EWR (2007) Modelled impact of future climate change on the phenology of winegrapes in Australia. Austr J Grape Wine Res 13: 165-175.
79. Webb LB, Whetton PH, Barlow EWR (2008) Climate change and winegrape quality in Australia. Clim Res 36: 99-111.
80. Webb LB, Dunn G, Barlow EWR (2010) Adapting agriculture to climate change: preparing Australian agriculture, forestry and fisheries for the future. In: Stokes CJ, Howden SM (eds) Viticulture. CSIRO Publishing, Melbourne.
81. Wilczek AM, Burghardt LT, Cobb AR, Cooper MD, Welch SM, Schmitt J (2010) Genetic and physiological bases for phenological responses to current and predicted climates. Philos Trans R Soc B Biol Sci 365: 3129-3147.
82. Wu S, Xiao H, Cabrera A, Meulia T, van der Knaap E (2011) SUN regulates vegetative and reproductive organ shape by changing cell division patterns. Plant Physiol 157: 1175-1186.