Improving fruit and wine: what does genomics have to offer?

Viala, 1901 Collard, 2008, Marker-assisted selection: an approach for precision plant breeding in the twenty-first century, Philos. Trans. R. Soc. B: Biol. Sci., 363, 557, 10.1098/rstb.2007.2170 Ignatov, 2011, Malus, 45 Kellerhals, 2000, Marker-assisted selection in apple breeding, Acta Hort., 521, 255, 10.17660/ActaHortic.2000.521.28 Dirlewanger, 2004, Comparative mapping and marker-assisted selection in Rosaceae fruit crops, Proc. Natl. Acad. Sci. U.S.A., 101, 9891, 10.1073/pnas.0307937101 di Gaspero, 2010, Application of genomics to grapevine improvement, Aust. J. Grape Wine Res., 16, 122, 10.1111/j.1755-0238.2009.00072.x Bus, 2000, Marker-assisted selection for pest and disease resistance in the New Zealand apple breeding program, Acta Hort., 538, 541, 10.17660/ActaHortic.2000.538.95 Shulaev, 2008, Multiple models for Rosaceae genomics, Plant Physiol., 147, 985, 10.1104/pp.107.115618 Tartarini, 2003, The use of molecular markers in pome fruit breeding, Acta Hort., 622, 129, 10.17660/ActaHortic.2003.622.11 Korban, 2009, Apple structural genomics, 85 King, 1999, Introgression of the Vf source of scab resistance and distribution of linked marker alleles within the Malus gene pool, Theor. Appl. Genet., 99, 1039, 10.1007/s001220051412 Hemmat, 2003, Identification and mapping of markers for resistance to apple scab from ‘Antonovka’ and ‘Hansen's baccata #2’, Acta Hort., 622, 153, 10.17660/ActaHortic.2003.622.13 Evans, 2003, Identification of SCAR markers linked to Pl-w mildew resistance in apple, Theor. Appl. Genet., 106, 1178, 10.1007/s00122-002-1147-2 Khan, 2007, Development of molecular markers linked to the Fiesta linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection, Genome, 50, 568, 10.1139/G07-033 Peil, 2007, Strong evidence for a fire blight resistance gene of Malus robusta located on linkage group 3, Plant Breed., 126, 470, 10.1111/j.1439-0523.2007.01408.x Riaz, 2009, Using marker-assisted selection to breed Pierce's disease-resistant grapes, Am. J. Enol. Viticult., 60, 199, 10.5344/ajev.2009.60.2.199 Mahanil, 2012, Development of marker sets useful in the early selection of Ren4 powdery mildew penetration resistance and seedlessness for table and raisin grape breeding, Theor. Appl. Genet., 124, 23, 10.1007/s00122-011-1684-7 This, 2007, Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1, Theor. Appl. Genet., 114, 723, 10.1007/s00122-006-0472-2 Dalbo, 2000, A gene controlling sex in grapevines placed on a molecular marker-based genetic map, Genome, 43, 333, 10.1139/g99-136 Marguerit, 2009, Genetic dissection of sex determinism, inflorescence morphology and downy mildew resistance in grapevine, Theor. Appl. Genet., 118, 1261, 10.1007/s00122-009-0979-4 Doligez, 2002, Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight, Theor. Appl. Genet., 105, 780, 10.1007/s00122-002-0951-z Emanuelli, 2010, A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.), BMC Plant Biol., 10, 241, 10.1186/1471-2229-10-241 Donnelly, 2008, Progress and challenges in genome-wide association studies in humans, Nature, 456, 728, 10.1038/nature07631 Zhao, 2011, Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa, Nat. Commun., 2, 467, 10.1038/ncomms1467 Tian, 2011, Genome-wide association study of leaf architecture in the maize nested association mapping population, Nat. Genet., 43, 159, 10.1038/ng.746 Huang, 2010, Genome-wide association studies of 14 agronomic traits in rice landraces, Nat. Genet., 42, 961, 10.1038/ng.695 Atwell, 2010, Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines, Nature, 465, 627, 10.1038/nature08800 Myles, 2009, Association mapping: critical considerations shift from genotyping to experimental design, Plant Cell, 21, 2194, 10.1105/tpc.109.068437 Pimentel, 1997, Economic and environmental benefits of biodiversity, BioScience, 47, 747, 10.2307/1313097 Bernardo, 2010 Hamblin, 2011, Population genetics of genomics-based crop improvement methods, Trends Genet., 27, 98, 10.1016/j.tig.2010.12.003 Nordborg, 2008, Next-generation genetics in plants, Nature, 456, 720, 10.1038/nature07629 McMullen, 2009, Genetic properties of the maize nested association mapping population, Science, 325, 737, 10.1126/science.1174320 Robinson, 2006 Myles, 2011, Genetic structure and domestication history of the grape, Proc. Natl. Acad. Sci. U.S.A., 108, 3530, 10.1073/pnas.1009363108 Laucou, 2011, High throughput analysis of grape genetic diversity as a tool for germplasm collection management, Theor. Appl. Genet., 122, 1233, 10.1007/s00122-010-1527-y Noiton, 1996, Founding clones, inbreeding, coancestry, and status number of modern apple cultivar, J. Am. Soc. Hort. Sci., 121, 773, 10.21273/JASHS.121.5.773 Bryc, 2010, Genome-wide patterns of population structure and admixture in West Africans and African Americans, Proc. Natl. Acad. Sci. U.S.A., 107, 786, 10.1073/pnas.0909559107 Tang, 2006, Reconstructing genetic ancestry blocks in admixed individuals, Am. J. Hum. Genet., 79, 1, 10.1086/504302 Wegmann, 2011, Recombination rates in admixed individuals identified by ancestry-based inference, Nat. Genet., 43, 847, 10.1038/ng.894 Heffner, 2009, Genomic selection for crop improvement, Crop Sci., 49, 1, 10.2135/cropsci2008.08.0512 Kumar, 2012, Towards genomic selection in apple (Malus x domestica Borkh.) breeding programmes: prospects, challenges and strategies, Tree Genet. Genomes, 8, 1, 10.1007/s11295-011-0425-z Kumar, 2012, Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.), PLoS ONE, 7, e36674, 10.1371/journal.pone.0036674 Myles, 2010, Rapid genomic characterization of the genus Vitis, PLoS ONE, 5, e8219, 10.1371/journal.pone.0008219 Chagné, 2012, Genome-wide SNP detection, validation, and development of an 8K SNP array for apple, PLoS ONE, 7, e31745, 10.1371/journal.pone.0031745 Micheletti, 2011, Genetic diversity of the genus Malus and implications for linkage mapping with SNPs, Tree Genet. Genomes, 7, 857, 10.1007/s11295-011-0380-8 Lijavetzky, 2007, High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology, BMC Genomics, 8, 424, 10.1186/1471-2164-8-424 Morgante, 2005, Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize, Nat. Genet., 37, 997, 10.1038/ng1615 Springer, 2009, Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content, PLoS Genet., 5, e1000734, 10.1371/journal.pgen.1000734 Kim, 2010, Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome, Proc. Natl. Acad. Sci. U.S.A., 107, 22032, 10.1073/pnas.1009526107 Elshire, 2011, A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species, PLoS ONE, 6, e19379, 10.1371/journal.pone.0019379 Baird, 2008, Rapid SNP discovery and genetic mapping using sequenced RAD markers, PLoS ONE, 3, e3376, 10.1371/journal.pone.0003376 Poland, 2012, Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach, PLoS ONE, 7, e32253, 10.1371/journal.pone.0032253 Peterson, 2012, Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species, PLoS ONE, 7, e37135, 10.1371/journal.pone.0037135 Davey, 2011, Genome-wide genetic marker discovery and genotyping using next-generation sequencing, Nat. Rev. Genet., 12, 499, 10.1038/nrg3012 Kijas, 2009, A genome wide survey of SNP variation reveals the genetic structure of sheep breeds, PLoS ONE, 4, e4668, 10.1371/journal.pone.0004668 Verde, 2012, Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP Detection and validation in breeding germplasm, PLoS ONE, 7, e35668, 10.1371/journal.pone.0035668 Pasaniuc, 2012, Extremely low-coverage sequencing and imputation increases power for genome-wide association studies, Nat. Genet., 44, 631, 10.1038/ng.2283 1000 Genomes Project Consortium, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534 Luby, 2001, Does marker-assisted selection make dollars and sense in a fruit breeding program?, HortScience, 36, 872, 10.21273/HORTSCI.36.5.872 McKenna, 2010, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 Lu, 2013, Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol, PLoS Genet, 9, e1003215, 10.1371/journal.pgen.1003215 Morgante, 2006, Plant genome organisation and diversity: the year of the junk!, Curr. Opin. Biotechnol., 17, 168, 10.1016/j.copbio.2006.03.001 Morgante, 2007, Transposable elements and the plant pan-genomes, Curr. Opin. Plant Biol., 10, 149, 10.1016/j.pbi.2007.02.001