본문 바로가기
KERD
논문KCI 등재

포도 유전체 연구현황 및 전망

Current status and prospects of genomics and bioinformatics in grapes

2

조회

0

다운로드

7

인용

0

참고문헌

키워드

주제분류농학

초록

Grape is one of the important fruit crops around the world, and exposed to disease and pests, and internal or environmental stresses in the vineyards. Breeding and cultivation of new varieties of high quality-grapes resistant to diseases and pests and tolerant to stresses are the most important steps in the grape production. However, conventional breeding has laborious and time-consuming procedures in maintaining and selecting seedlings in the fields. Development of molecular breeding technology through understanding of molecular mechanism of useful traits can be used as an alternative strategy to improve the efficiency of grape breeding program by cross hybridization in grape development programs. The completion of the grape genome sequencing project provided the way to discover the novel genes and to analyze their functions. Comparative genomics, transcriptomic analysis, and the genome-wide identification and analysis of useful genes as well as development of molecular marker for valuable traits could provide novel insights into fruit quality and the responses to diseases and stresses, and can be used as important information in molecular breeding programs for grape development.

Abstract

Grape is one of the important fruit crops around the world, and exposed to disease and pests, and internal or environmental stresses in the vineyards. Breeding and cultivation of new varieties of high quality-grapes resistant to diseases and pests and tolerant to stresses are the most important steps in the grape production. However, conventional breeding has laborious and time-consuming procedures in maintaining and selecting seedlings in the fields. Development of molecular breeding technology through understanding of molecular mechanism of useful traits can be used as an alternative strategy to improve the efficiency of grape breeding program by cross hybridization in grape development programs. The completion of the grape genome sequencing project provided the way to discover the novel genes and to analyze their functions. Comparative genomics, transcriptomic analysis, and the genome-wide identification and analysis of useful genes as well as development of molecular marker for valuable traits could provide novel insights into fruit quality and the responses to diseases and stresses, and can be used as important information in molecular breeding programs for grape development.

참고문헌 (121)

  1. Adam-Blondon AF, "Usefulness of two SCAR markers for marker-assisted selection of seedless grapevine cultivars", Vitis, 40, pp.147~155 (2001)
  2. Adam-Blondon AF, "Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics", Theor Appl Genet, 109, pp.1017~1027 (2004)
  3. Ahn SY, "De novo transcriptome analysis of Vitis flexuosa grapevine inoculated with Elsinoe ampelina", Plant Genet Resour-Charact Util, 12, pp.S130~S133 (2014)
  4. Azuma A, "Haplotype composition at the color locus is a major genetic determinant of skin color variation in Vitis×labruscana grapes", Theor Appl Genet, 122, pp.1427~1438 (2011)
  5. Barba P, "Vitis rupestris B38 confers isolate-specific quantitative resistance to penetration by Erysiphe nector", Phytopathology, 105, pp.1097~1103 (2015)
  6. Barba P, "Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map", Theor Appl Genet, 127, pp.73~84 (2014)
  7. Barka EA, "Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN", Appl Environ Microbiol, 72, pp.7246~7255 (2006)
  8. Bellin D, "Resistance to Plasmopara viticola in grapevine ‘Bianca’ is controlled by a major dominant gene causing localised necrosis at the infection site", Theor Appl Genet, 120, pp.163~176 (2009)
  9. Berli F, "Phenolic composition in grape (Vitis vinifera L. cv. Malbec) ripened with different solar UV-B radiation levels by capillary zone electrophoresis", J Agric Food Chem, 56, pp.2892~2898 (2008)
  10. Berli F, "Abscisic acid is involved in the response of grape (Vitis vinifera L.) cv. Malbec leaf tissues to ultraviolet-B radiation by enhancing ultraviolet-absorbing compounds, antioxidant enzymes and membrane sterols", Plant Cell Environ, 33, pp.1~10 (2009)
  11. Bert PF, "Mapping genetic loci for tolerance to lime-induced iron deficiency chlorosis in grapevine rootstocks (Vitis sp.)", Theor Appl Genet, 126, pp.451~473 (2013)
  12. Blanc S, "A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew", Theor Appl Genet, 125, pp.1663~1675 (2012)
  13. Bornman JF, "Plants and UV-B: Responses to Environmental Change", pp.157~168 (1997), Cambridge University Press
  14. Bouquet A, "Contribution à l’étude de l’espèce Muscadinia rotundifolia (Michx) Small et de ses hybrides avec Vitis vinifera L. Applications en sélection", Doct, pp.1983
  15. Bouquet A, "Inheritance of seedlessness in grapevine (Vitis vinifera L.)", Vitis, 35, pp.35~42 (1996)
  16. Bouquet A, "Introduction dans l’spece Vitis vinifera :L. d’un caracterebde resistance a l’oidium (Uncinula necator Schw. Burr.) issu de l’espece Muscadinia rotundifoloia (Michx)Small", Vignevini, 13(12), pp.141~146 (1986)
  17. Brosché M, "Molecular events following perception of ultraviolet-B radiation by plants", Physiol Plant, 117, pp.1~10 (2003)
  18. Cabezas JA, "A genetic analysis of seed and berry weight in grapevine", Genome, 49, pp.1572~7585 (2006)
  19. Caprio JM, "Weather conditions associated with grape production in the Okanagan Valley of British Columbia and potential impact of climate change", Can J Plant Sci, 82, pp.755~763 (2002)
  20. Chaves MM, "Deficit irrigation in grapevine improves water-use efficiency while controlling vigour and production quality", Ann Appl Biol, 150, pp.237~252 (2007)
  21. Chen J, "Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries", BMC Plant Biol, 15, pp.28~ (2015)
  22. Coleman C, "The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines", BMC genetics, 10, pp.89~ (2009)
  23. Coombe, B.G., "Dynamics of grape berry growth and physiology of ripening", Austr J Grape Wine Res, 6, pp.131~135 (2000)
  24. Cramer GR, "Abiotic stress and plant responses from the whole vine to the genes", Austr J Grape Wine Res, 16, pp.86~93 (2010)
  25. Cramer GR, "Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles", Funct Integr Genomics, 7, pp.111~134 (2007)
  26. Cramer GR, "Effects of abiotic stress on plants: a systems biology perspective", BMC Plant Biol, 11, pp.163~ (2011)
  27. Crane O, "Cytokinin-induced VvTFL1A expression may be involved in the control of grapevine fruitfulness", 235, pp.181~192 (2012)
  28. Dalbo MA, "Marker-assisted selection for powdery mildew resistance in grapes", J Am Soc Hortic Sci, 126, pp.83~89 (2001)
  29. Deluc LG, "Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development", BMC Genomics, 8, pp.429~ (2007)
  30. Di Gaspero G, "Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers from R-gene candidates", Theor Appl Genet, 114, pp.1249~1263 (2007)
  31. Doligez A, "Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight", Theor Appl Genet, 105, pp.780~795 (2002)
  32. Emanuelli F, "Development of user-friendly functional molecular markers for VvDXS gene conferring muscat flavor in grapevine", Mol Breeding, 33, pp.235~241 (2014)
  33. Emmanuelli F, "Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape", BMC Plant Biol, 13, pp.39~ (2013)
  34. Espinoza C, "Gene expression associated with compatible viral diseases in grapevine cultivars", Funct Integr Genomics, 7, pp.95~110 (2007)
  35. "Food and agricultural commodities production" (2014)[URL]
  36. Feechan A, "Genetic dissection of a TIR-NB-LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathogens in cultivated grapevine", Plant J, 76, pp.661~674 (2013)
  37. Figueiredo A, "Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi", J Exp Bot, 59, pp.3371~3381 (2008)
  38. Fortes AM, "Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening", BMC Plant Biol, 11, pp.149~ (2011)
  39. Frohnmeyer H, "Ultraviolet-B radiation-mediated responses in plants. Balancing damage and protection", Plant Physiol, 133, pp.1420~1428 (2003)
  40. Fuller MP, "An investigation of the frost hardiness of grapevine (Vitis vinifera) during bud break", Annu Appl Biol, 135, pp.589~595 (1999)
  41. Gao M, "Characterization of Erysiphe nector-responsive genes in Chinese wild Vitis quinquangularis", Intl J Mol Sci, 13, pp.11497~11519 (2012)
  42. Genova AD, "Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants", BMC Plant Biol, 14, pp.7~ (2014)
  43. Guillaumie S, "Transcriptional analysis of late ripening stages of grapevine berry", BMC Plant Biol, 11, pp.165~ (2011)
  44. He N, "Grape breeding for cold resistance in northeast China for 30 years", Proc. of 5th International Symposium on grape breeding, pp.329~ (1990), Vitis special issue
  45. Hemstad, P.R., "Utilization of Vitis riparia for the development of new wine varieties with resistance to disease and extreme cold", Acta Hortic, 528, pp.487~490 (2000)
  46. Hoffmann S, "Resistance to Erysiphe necator in the grapevine 'Kishmish vatkana' is controlled by a single locus through restriction of hyphal growth", Theor Appl Genet, 116, pp.427~438 (2008)
  47. Howell GS, "Sustainable grape productivity and the growth-yield relationship: A review", Am J Enol Vitic, 52, pp.165~174 (2001)
  48. 허윤영, "RAPD와 SSR 마커를 이용한 포도 대목 품종 및 포도 속(Vitis) 야생 유전자원의 유연관계 분석", 한국육종학회지, 44(1), pp.19~28 (2012), 한국육종학회
  49. Hur YY, "Changes of leaf water potential and CO2 assimilation in Korean native Vitis flexuosa during drought and subsequent recovery", Proc. of 28th International Horticultural Congress, pp.724~ (2010), Abstract Ⅱ
  50. 허윤영, "포도 무핵 유전자원의 유연관계 분석 및 무핵 형질과 연관된 P3_VvAGL11 마커의 활용성 평가", 한국육종학회지, 46(1), pp.28~36 (2014), 한국육종학회[DOI]
  51. Hyma KE, "Heterozygous mapping strategy (HetMappS) for high resolution genotypingby-sequencing markers: a case study in grapevine", PLoS ONE, 10(8), pp.e0134880~ (2015)
  52. Jaillon O, "The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla", Nature, 449, pp.463~467 (2007)
  53. Jansen MAK, "Higher plants and UV-B radiation: balancing damage, repair and acclimation", Trends Plant Sci, 3, pp.131~135 (1998)
  54. Jenkins GI, "Signal transduction in responses to UV-B radiation", Annu Rev Plant Biol, 60, pp.407~431 (2009)
  55. Jung CJ, "Gibberellin application at pre-bloom in grapevines down-regulates the expressions of VvIAA9 and VvARF7, negative regulators of fruit set initiation, during parthenocarpic fruit development", PLoS ONE, 9(4), pp.e95634~ (2014)
  56. Kim ES, Chang EH, Hur YY, Kim TW, "Jung SM(2015a)Anthocyanin contents and composition of VlmybA1-2 and VlmybA2 genes in Vitis labrusca hybrid grape cultivars and cross seedlings", Plant Omics J, 8, pp.472~478
  57. Kim GH, "Identification of AFLP and RAPD markers linked to anthracnose resistance in grapes and their conversion to SCAR markers", Plant Breeding, 127, pp.418~423 (2008)
  58. 김선애, "Differential Expression Screening of Defense Related Genes in Dormant Buds of Cold-Treated Grapevines", Plant Breeding and Biotechnology, 1(1), pp.14~23 (2013), 한국육종학회[DOI]
  59. Kim SA, "Expression of genes affecting skin coloration and sugar accumulation in grape berries at ripening stages under high temperatures", Adv Environ Res, 87, pp.25~31 (2015)
  60. Kim SA, "Transcription analysis of grapevines exposed to low temperature" (2016), Hort Environ Biotechnol
  61. Kobayashi S, "Retrotransposon induced mutations in grape skin color", Science, 304, pp.982~ (2004)
  62. Kriedemann PE, "Photosynthesis in vine leaves as a function of light intensity, temperature, and leaf age", Vitis, 7, pp.213~220 (1986)
  63. Lahogue F, "Identification of a codominant SCAR marker linked to the seedlessness character in grapevine", Theor Appl Genet, 97, pp.950~959 (1998)
  64. Liu GT, "Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress", BMC Plant Biol, 12, pp.174~ (2012)
  65. Lodhi MA, "A molecular marker based linkage map of Vitis", Genome, 38, pp.786~794 (1995)
  66. Development and evaluation of cold hardy wine grape breeding selections and cultivars in the upper Midwest, "Luby JJ", AVERN, ~ (2003)
  67. Luo F, "Grape breeding in China", Proc. 5th International Symposium on grape breeding, pp.212~216 (1990)
  68. Luo HB, "Photosynthetic responses to heat treatments at different temperatures and following recovery in grapevine (Vitis amurensis L.) leaves", PLoS ONE, 6, pp.e23033~ (2011)
  69. Ma YY, "Differential physio-biochemical responses to cold stress of cold-tolerant and non-tolerant grapes (Vitis L.) from China", J Agro Crop Sci, 196, pp.212~219 (2010)
  70. Mahajan S, "Cold, salinity and drought stresses: an overview", Arch Biochem Biophys, 444, pp.139~158 (2005)
  71. Mandl K, "A genetic map of Welschriesling × Sirius for the identification of magnesium deficiency by QTL analysis", Euphytica, 149, pp.133~144 (2006)
  72. Mardis ER, "The impact of next-generation sequencing technology on genetics", Trends Gent, 24, pp.133~141 (2008)
  73. Mathiason K, "Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break", Funct Integr Genomics, 9, pp.81~96 (2009)
  74. Matus JT, "Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes", BMC Plant Biol, 8, pp.83~ (2008)
  75. Mejía N, "Identification of QTLs for seedlessness, berry size, and ripening date in a seedless table grape progeny", Am J Enol Vitic, 58, pp.499~507 (2007)
  76. Mejía N, "Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine", BMC Plant Biol, 11, pp.57~ (2011)
  77. Merdinoglu D, "Genetic Analysis of Downy mildew resistance derived from Muscadinia rotundifolia", Acta Hortic, 603, pp.451~456 (2003)
  78. Miller AJ, "Vitis phylogenomics: Hybridization intensities from a SNP array outperform genotype calls", PLoS ONE, 8, pp.e78680~ (2013)
  79. Moreira FM, "Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance", Tree Genet genomics, 7, pp.153~167 (2011)
  80. Mori K, "Loss of anthocyanins in red-wine grape under high temperature", J Exp Bot, 58, pp.1935~1945 (2007)
  81. Myles S, "Genetic structure and domestication history of the grape", PNAS, 108, pp.3530~ (2011)
  82. Myles S, "Rapid genomic characterization of the genus Vitis", PloS ONE, 5, pp.e8219~ (2010)
  83. Nakagawa S, "Studies on the use of Japanese native Vitis species for grape production. Osaka", Pref Univ Fac Agr Sci Rep (1991)
  84. Olmo HP, "Evolution of crop plants", pp.294~298 (1976), Longman
  85. Pearson RC, "Compendium of grape disease" (1998), APS Press
  86. Pelsy F, "An extensive study of the genetic diversity within seven French wine grape variety collections", Theor Appl Genet, 120, pp.1219~1231 (2010)
  87. Perrone I, "Recovery from water stress affects grape leaf petiole transcriptome", Planta, 235, pp.1383~1396 (2012)
  88. Pilati S, "Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison", BMC Genomics, 8, pp.428~ (2007)
  89. Pontin MA, "Transcriptome changes in grapevines (Vitis vinifera L.) cv. Malbec leaves induced by ultraviolet-B radiation", BMC Plant Biol, 21, pp.224~ (2010)
  90. Ramming DW, "A single dominant locus, Ren4, confers rapid non-race-specific resistance to grapevine powdery mildew", Phytopathology, 101, pp.502~508 (2011)
  91. Reisch BI, "Fruit breeding; Handbook of plant breeding", pp.225~262 (2012), Springer
  92. Rex F, "QTL mapping of black rot (Guignardia bidwellii) resistance in the grapevine rootstock ‘Börner’ (V. riparia Gm183 × V. cinerea Arnold)", Theor Appl Genet, 127, pp.1667~1677 (2014)
  93. Riaz S, "A microsatellite marker based framewark linkage map of Vitis vinifera L", Theor Appl Genet, 108, pp.864~872 (2004)
  94. Riaz S, "Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (Erysiphe necator) and their use in marker-assisted breeding", Theor Appl Genet, 122, pp.1059~1073 (2011)
  95. Riaz S, "Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (Erysiphe necator) and their use in marker-assisted breeding", Theor Appl Genet, 122, pp.1059~1073 (2011)
  96. Rozema J, "UV-B as an environmental factor in plant life: stress and regulation", Trends Ecol Evol, 12, pp.22~28 (1997)
  97. Schultz HR, "Climate change and world viticulture. Cost Action 858 Workshop: Vineyard under environmental constraints: adaptations to climate change" (2007), University of Lodz
  98. Seki M, "Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray", Plant J, 31, pp.279~292 (2002)
  99. Sweetman C, "Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression", BMC Genomics, 13, pp.691~ (2012)
  100. Tattersall EAR, "Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress", Funct Intergr Genomics, 7, pp.317~333 (2007)
  101. Terrier N, "Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.)development", Planta, 222, pp.832~847 (2005)
  102. The Angiosperm Phylogeny Group, "An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG Ⅲ", Botanical Journal of the Linnean Society, 161, pp.105~121 (2009)
  103. The French-Italian Public Consortium for Grapevine Genome Characterization, "The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla", Nature, 449, pp.463~468 (2007)
  104. This P, "Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1", Theor Appl Genet, 114, pp.723~730 (2007)
  105. This P, "Historical origins and genetic diversity of wine grapes", Trends Genet, 22, pp.511~519 (2006)
  106. Ulm R, "Signaling and gene regulation in response to ultraviolet light", Curr Opin Plant Biol, 8, pp.477~482 (2005)
  107. van Leeuwen C, "Influence of climate, soil, and cultivar on terroir", Am J Enol Vitic, 55, pp.207~217 (2004)
  108. Velasco R, "A high quality draft consensus sequence of the genome of a heterozygous grapevine variety", PLoS One, 2, pp.e1326~ (2007)
  109. Vezzulli S, "A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501SNP-based markers", Theor Appl Genet, 117, pp.499~511 (2008)
  110. Wahid A, "Heat tolerance in plants: An overview", Environ Exp Bot, 161, pp.199~223 (2007)
  111. Wang L, "Molecular characteristics and biochemical functions of VpPR10s from Vitis pseudoreticulata associated with biotic and abiotic stresses", Intl J Mol Sci, 15, pp.19162~19182 (2014)
  112. Wang L, "Salicylic acid-induced heat or cold tolerance in relation to Ca2+ homeostasis and antioxidant systems in young grape plants", Plant Sci, 170, pp.685~694 (2006)
  113. Wang L, "Heat acclimation induced acquired heat tolerance and cross adaptation in different grape cultivars:Relationships to photosynthetic energy partitioning", Funct Plant Biol, 36, pp.516~526 (2009)
  114. Waters DL, "cDNA microarray analysis of developing grape (Vitis vinifera cv. Shiraz) berry skin", Funct Integr Genomics, 5, pp.40~58 (2005)
  115. Welter LJ, "Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L.)", Mol Breeding, 20, pp.359~374 (2007)
  116. Wu J, "Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology", BMC Plant Biol, 10, pp.234~ (2010)
  117. Xin H, "Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress", PLoS ONE, 8, pp.3~ (2013)
  118. Xu J, "Next-generation sequencing: Current Technologies and Applications" (2014), Caister Academic Press
  119. Xu W, "Transcriptome profiling of Vitis amurensis, an extremely cold‑tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress", Plant Mol Biol, 86, pp.527~541 (2014)
  120. Zenoni S, "Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq", Plant Physiol, 152, pp.1787~1795 (2010)
  121. Zharkikh A, "Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: problems and solutions", J Biotechnol, 136, pp.38~43 (2008)

관련 논문AI추천

이 간행물의 다른 논문 (17건)