Structural and functional apple genomics and its application in breeding S.E. (2018): Structural and functional apple genomics and its application in breeding. Czech J. Genet. Plant Breed., 54: 147-153.
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The present paper summarized some knowledge of modern technologies, applied in apple (Malus domestica) genome studies. New generation sequencing allowed single nucleotide polymorphism (SNP) chip technologies for genotyping, description of functional apple genes, characterization of the evolutionary results in apple genome fragment transition, as well as phylogenetic reconstruction of the genus Malus, being the confirmed progeny of M. sieviersii. Based on these technologies, newly developed putative markers may give the most important biological data such as age, geographical origins, tissue type determination, and external visible characters. The new generation genotyping platforms, representing very high efficiency, are now successfully applied for random apple genome-wide association (GWA) studies as well pedigree-based analysis and marker-assisted selection (MAS).

Bai Yang, Dougherty Laura, Xu Kenong (2014): Towards an improved apple reference transcriptome using RNA-seq. Molecular Genetics and Genomics, 289, 427-438
Baldo Angela, Norelli Jay L, Farrell Robert E, Bassett Carole L, Aldwinckle Herb S, Malnoy Malnoy (2010): Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus × domestica) with Erwinia amylovora. BMC Plant Biology, 10, 1-
Bianco Luca, Cestaro Alessandro, Sargent Daniel James, Banchi Elisa, Derdak Sophia, Di Guardo Mario, Salvi Silvio, Jansen Johannes, Viola Roberto, Gut Ivo, Laurens Francois, Chagné David, Velasco Riccardo, van de Weg Eric, Troggio Michela, Jaiswal Pankaj (2014): Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh). PLoS ONE, 9, e110377-
Bianco Luca, Cestaro Alessandro, Linsmith Gareth, Muranty Hélène, Denancé Caroline, Théron Anthony, Poncet Charles, Micheletti Diego, Kerschbamer Emanuela, Di Pierro Erica A., Larger Simone, Pindo Massimo, Van de Weg Eric, Davassi Alessandro, Laurens François, Velasco Riccardo, Durel Charles-Eric, Troggio Michela (2016): Development and validation of the Axiom ® Apple480K SNP genotyping array. The Plant Journal, 86, 62-74
Boocock James, Chagné David, Merriman Tony R., Black Michael A. (2015): The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. BMC Genomics, 16, -
Chagné David, Carlisle Charmaine M, Blond Céline, Volz Richard K, Whitworth Claire J, Oraguzie Nnadozie C, Crowhurst Ross N, Allan Andrew C, Espley Richard V, Hellens Roger P, Gardiner Susan E (): Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics, 8, 212-
Chagné David, Crowhurst Ross N., Troggio Michela, Davey Mark W., Gilmore Barbara, Lawley Cindy, Vanderzande Stijn, Hellens Roger P., Kumar Satish, Cestaro Alessandro, Velasco Riccardo, Main Dorrie, Rees Jasper D., Iezzoni Amy, Mockler Todd, Wilhelm Larry, Van de Weg Eric, Gardiner Susan E., Bassil Nahla, Peace Cameron, Bendahmane Mohammed (2012): Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple. PLoS ONE, 7, e31745-
Chagne D., Lin-Wang K., Espley R. V., Volz R. K., How N. M., Rouse S., Brendolise C., Carlisle C. M., Kumar S., De Silva N., Micheletti D., McGhie T., Crowhurst R. N., Storey R. D., Velasco R., Hellens R. P., Gardiner S. E., Allan A. C. (2012): An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes. PLANT PHYSIOLOGY, 161, 225-239
Clarke Joseph D., Zhu Tong (2006): Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. The Plant Journal, 45, 630-650
Conrad Donald F., Pinto Dalila, Redon Richard, Feuk Lars, Gokcumen Omer, Zhang Yujun, Aerts Jan, Andrews T. Daniel, Barnes Chris, Campbell Peter, Fitzgerald Tomas, Hu Min, Ihm Chun Hwa, Kristiansson Kati, MacArthur Daniel G., MacDonald Jeffrey R., Onyiah Ifejinelo, Pang Andy Wing Chun, Robson Sam, Stirrups Kathy, Valsesia Armand, Walter Klaudia, Wei John, Tyler-Smith Chris, Carter Nigel P., Lee Charles, Scherer Stephen W., Hurles Matthew E. (2010): Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712
Eisen M.B., Brown P.O. (1999): DNA arrays for analysis of gene expression. Methods in Enzymology, 303: 179–205.
Ekblom R, Galindo J (2011): Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107, 1-15
Gapper Nigel E, Giovannoni James J, Watkins Christopher B (2014): Understanding development and ripening of fruit crops in an ‘omics’ era. Horticulture Research, 1, -
Girardi César Luís, Rombaldi César Valmor, Dal Cero Joceani, Nobile Paula M., Laurens François, Bouzayen Mondher, Quecini Vera (2013): Genome-wide analysis of the AP2/ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis. Scientia Horticulturae, 151, 112-121
Goulao Luis F., Oliveira Cristina M. (2007): Molecular identification of novel differentially expressed mRNAs up-regulated during ripening of apples. Plant Science, 172, 306-318
Han Yuepeng, Korban Schuyler S. (2008): An overview of the apple genome through BAC end sequence analysis. Plant Molecular Biology, 67, 581-588
Jakovljevic V., Otten P., Berwarth C., Jelkmann W. (2017): Analysis of the apple rubbery wood disease by next generation sequencing of total RNA. European Journal of Plant Pathology, 148, 637-646
Janssen Bart J, Thodey Kate, Schaffer Robert J, Alba Rob, Balakrishnan Lena, Bishop Rebecca, Bowen Judith H, Crowhurst Ross N, Gleave Andrew P, Ledger Susan, McArtney Steve, Pichler Franz B, Snowden Kimberley C, Ward Shayna (2008): Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biology, 8, 16-
Kamber T., Buchmann J.P., Porthier J.F., Smits T.H.M., Wicker T., Duffy B. (2016): Fire blight disease reactome: RNA seq transcriptional profile of apple host plant defense response to Erwinia amylovora pathogen infection. Nature: Scientific Reports, 6: 21600.
Khan M. Awais, Han Yuepeng, Zhao Youfu Frank, Korban Schuyler S. (2012): A high-throughput apple SNP genotyping platform using the GoldenGate™ assay. Gene, 494, 196-201
Koboldt Daniel C., Steinberg Karyn Meltz, Larson David E., Wilson Richard K., Mardis Elaine R. (2013): The Next-Generation Sequencing Revolution and Its Impact on Genomics. Cell, 155, 27-38
Krost Clemens, Petersen Romina, Schmidt Erwin R. (2012): The transcriptomes of columnar and standard type apple trees (Malus x domestica) — A comparative study. Gene, 498, 223-230
Krost Clemens, Petersen Romina, Lokan Stefanie, Brauksiepe Bastienne, Braun Peter, Schmidt Erwin R. (2013): Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies. Plant Molecular Biology, 81, 211-220
Kumar S., Chagne D., Bink M.C.A., Volz R.K., Whitwirth C., Carlisle C. (2012a): Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.). PLoS ONE, 7: e36674.
Kumar S., Banks T.W., Cloutier S. (2012b): SNP discovery through next-generation sequencing and its application. International Journal of Plant Genomics, 831460: 1–15.
Kumar Satish, Garrick Dorian J, Bink Marco CAM, Whitworth Claire, Chagné David, Volz Richard K (2013): Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics, 14, 393-
Leforestier Diane, Ravon Elisa, Muranty Hélène, Cornille Amandine, Lemaire Christophe, Giraud Tatiana, Durel Charles-Eric, Branca Antoine (2015): Genomic basis of the differences between cider and dessert apple varieties. Evolutionary Applications, 8, 650-661
Lehman I. Robert (2008): Historical perspective: Arthur Kornberg, a giant of 20th century biochemistry. Trends in Biochemical Sciences, 33, 291-296
Lehman I.R., Bessman M.J., Simms E.S., Kornberg A. (1958): Enzymatic synthesis of deoxyribonucleic acid. (I). Preparation of substrates and partial purification of an enzyme from Escherichia coli. The Journal of Biological Chemistry, 233: 163–170.
Linnarsson Sten (2010): Recent advances in DNA sequencing methods – general principles of sample preparation. Experimental Cell Research, 316, 1339-1343
Liu Yuanxia, Lan Jinhao, Li Qing, Zhang Yugang, Wang Caihong, Dai Hongyi (2017): Rapid location of Glomerella leaf spot resistance gene locus in apple by whole genome re-sequencing. Molecular Breeding, 37, -
Lopez-Maestre Hélène, Brinza Lilia, Marchet Camille, Kielbassa Janice, Bastien Sylvère, Boutigny Mathilde, Monnin David, Filali Adil El, Carareto Claudia Marcia, Vieira Cristina, Picard Franck, Kremer Natacha, Vavre Fabrice, Sagot Marie-France, Lacroix Vincent (): SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Research, , gkw655-
Maliepaard C., Alston F. H., van Arkel G., Brown L. M., Chevreau E., Dunemann F., Evans K. M., Gardiner S., Guilford P., van Heusden A. W., Janse J., Laurens F., Lynn J. R., Manganaris A. G., den Nijs A. P. M., Periam N., Rikkerink E., Roche P., Ryder C., Sansavini S., Schmidt H., Tartarini S., Verhaegh J. J., Vrielink-van Ginkel M., King G. J. (1998): Aligning male and female linkage maps of apple ( Malus pumila Mill.) using multi-allelic markers. TAG Theoretical and Applied Genetics, 97, 60-73
Maxam A. M., Gilbert W. (1977): A new method for sequencing DNA.. Proceedings of the National Academy of Sciences, 74, 560-564
Micheletti Diego, Troggio Michela, Zharkikh Andrey, Costa Fabrizio, Malnoy Mickael, Velasco Riccardo, Salvi Silvio (2011): Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genetics & Genomes, 7, 857-868
Muñoz-Amatriaín María, Eichten Steven R, Wicker Thomas, Richmond Todd A, Mascher Martin, Steuernagel Burkhard, Scholz Uwe, Ariyadasa Ruvini, Spannagl Manuel, Nussbaumer Thomas, Mayer Klaus FX, Taudien Stefan, Platzer Matthias, Jeddeloh Jeffrey A, Springer Nathan M, Muehlbauer Gary J, Stein Nils (2013): Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biology, 14, -
Newcomb R. D. (2006): Analyses of Expressed Sequence Tags from Apple. PLANT PHYSIOLOGY, 141, 147-166
Ozsolak Fatih, Ting David T, Wittner Ben S, Brannigan Brian W, Paul Suchismita, Bardeesy Nabeel, Ramaswamy Sridhar, Milos Patrice M, Haber Daniel A (2010): Amplification-free digital gene expression profiling from minute cell quantities. Nature Methods, 7, 619-621
Patocchi A., Vinatzer B. A., Gianfranceschi L., Tartarini S., Zhang H.-B., Sansavini S., Gessler C. (1999): Construction of a 550 kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf. Molecular and General Genetics MGG, 262, 884-891
Patocchi A., Fernández-Fernández F., Evans K., Gobbin D., Rezzonico F., Boudichevskaia A., Dunemann F., Stankiewicz-Kosyl M., Mathis-Jeanneteau F., Durel C. E., Gianfranceschi L., Costa F., Toller C., Cova V., Mott D., Komjanc M., Barbaro E., Kodde L., Rikkerink E., Gessler C., van de Weg W. E. (2009): Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome. Tree Genetics & Genomes, 5, 211-223
Russell Joanne, Hackett Christine, Hedley Pete, Liu Hui, Milne Linda, Bayer Micha, Marshall David, Jorgensen Linzi, Gordon Sandra, Brennan Rex (2014): The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences. Molecular Breeding, 33, 835-849
Sanger F., Coulson A.R. (1975): A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 94, 441-448
Sanger F., Nicklen S., Coulson A. R. (1977): DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74, 5463-5467
SHOKRALLA SHADI, SPALL JENNIFER L., GIBSON JOEL F., HAJIBABAEI MEHRDAD (2012): Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, 1794-1805
Shulaev Vladimir, Sargent Daniel J, Crowhurst Ross N, Mockler Todd C, Folkerts Otto, Delcher Arthur L, Jaiswal Pankaj, Mockaitis Keithanne, Liston Aaron, Mane Shrinivasrao P, Burns Paul, Davis Thomas M, Slovin Janet P, Bassil Nahla, Hellens Roger P, Evans Clive, Harkins Tim, Kodira Chinnappa, Desany Brian, Crasta Oswald R, Jensen Roderick V, Allan Andrew C, Michael Todd P, Setubal Joao Carlos, Celton Jean-Marc, Rees D Jasper G, Williams Kelly P, Holt Sarah H, Rojas Juan Jairo Ruiz, Chatterjee Mithu, Liu Bo, Silva Herman, Meisel Lee, Adato Avital, Filichkin Sergei A, Troggio Michela, Viola Roberto, Ashman Tia-Lynn, Wang Hao, Dharmawardhana Palitha, Elser Justin, Raja Rajani, Priest Henry D, Bryant Douglas W, Fox Samuel E, Givan Scott A, Wilhelm Larry J, Naithani Sushma, Christoffels Alan, Salama David Y, Carter Jade, Girona Elena Lopez, Zdepski Anna, Wang Wenqin, Kerstetter Randall A, Schwab Wilfried, Korban Schuyler S, Davik Jahn, Monfort Amparo, Denoyes-Rothan Beatrice, Arus Pere, Mittler Ron, Flinn Barry, Aharoni Asaph, Bennetzen Jeffrey L, Salzberg Steven L, Dickerman Allan W, Velasco Riccardo, Borodovsky Mark, Veilleux Richard E, Folta Kevin M (2011): The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43, 109-116
Soglio V., Costa F., Molthoff J. W., Weemen-Hendriks W. M. J., Schouten H. J., Gianfranceschi L. (2009): Transcription analysis of apple fruit development using cDNA microarrays. Tree Genetics & Genomes, 5, 685-698
Soria-Guerra Ruth Elena, Rosales-Mendoza Sergio, Gasic Ksenija, Wisniewski Michael E., Band Mark, Korban Schuyler S. (2011): Gene Expression is Highly Regulated in Early Developing Fruit of Apple. Plant Molecular Biology Reporter, 29, 885-897
Stryer L., Augustyniak J., Michejda J. (2003): Biochemia. Warszawa, Wydawnictwo Naukowe PWN. (in Polish)
Sun Rui, Chang Yuansheng, Yang Fengqiu, Wang Yi, Li Hui, Zhao Yongbo, Chen Dongmei, Wu Ting, Zhang Xinzhong, Han Zhenhai (2015): A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genomics, 16, -
Troggio M., Gleave A., Salvi S., Chagné D., Cestaro A., Kumar S., Crowhurst R. N., Gardiner S. E. (2012): Apple, from genome to breeding. Tree Genetics & Genomes, 8, 509-529
Velasco Riccardo, Zharkikh Andrey, Affourtit Jason, Dhingra Amit, Cestaro Alessandro, Kalyanaraman Ananth, Fontana Paolo, Bhatnagar Satish K, Troggio Michela, Pruss Dmitry, Salvi Silvio, Pindo Massimo, Baldi Paolo, Castelletti Sara, Cavaiuolo Marina, Coppola Giuseppina, Costa Fabrizio, Cova Valentina, Dal Ri Antonio, Goremykin Vadim, Komjanc Matteo, Longhi Sara, Magnago Pierluigi, Malacarne Giulia, Malnoy Mickael, Micheletti Diego, Moretto Marco, Perazzolli Michele, Si-Ammour Azeddine, Vezzulli Silvia, Zini Elena, Eldredge Glenn, Fitzgerald Lisa M, Gutin Natalia, Lanchbury Jerry, Macalma Teresita, Mitchell Jeff T, Reid Julia, Wardell Bryan, Kodira Chinnappa, Chen Zhoutao, Desany Brian, Niazi Faheem, Palmer Melinda, Koepke Tyson, Jiwan Derick, Schaeffer Scott, Krishnan Vandhana, Wu Changjun, Chu Vu T, King Stephen T, Vick Jessica, Tao Quanzhou, Mraz Amy, Stormo Aimee, Stormo Keith, Bogden Robert, Ederle Davide, Stella Alessandra, Vecchietti Alberto, Kater Martin M, Masiero Simona, Lasserre Pauline, Lespinasse Yves, Allan Andrew C, Bus Vincent, Chagné David, Crowhurst Ross N, Gleave Andrew P, Lavezzo Enrico, Fawcett Jeffrey A, Proost Sebastian, Rouzé Pierre, Sterck Lieven, Toppo Stefano, Lazzari Barbara, Hellens Roger P, Durel Charles-Eric, Gutin Alexander, Bumgarner Roger E, Gardiner Susan E, Skolnick Mark, Egholm Michael, Van de Peer Yves, Salamini Francesco, Viola Roberto (2010): The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics, 42, 833-839
Wang Zhong, Gerstein Mark, Snyder Michael (2009): RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57-63
Ward Judson A., Ponnala Lalit, Weber Courtney A. (2012): Strategies for transcriptome analysis in nonmodel plants. American Journal of Botany, 99, 267-276
WATSON J. D., CRICK F. H. C. (1953): Genetical Implications of the Structure of Deoxyribonucleic Acid. Nature, 171, 964-967
Wullschleger Stan D., Difazio Stephen P. (2003): Emerging Use of Gene Expression Microarrays in Plant Physiology. Comparative and Functional Genomics, 4, 216-224
Xu Yuting, Feng Shouqian, Jiao Qiqing, Liu Chaochao, Zhang Weiwei, Chen Weiyi, Chen Xuesen (2012): Comparison of MdMYB1 sequences and expression of anthocyanin biosynthetic and regulatory genes between Malus domestica Borkh. cultivar ‘Ralls’ and its blushed sport. Euphytica, 185, 157-170
Yang Shanshan, Fresnedo-Ramírez Jonathan, Wang Minghui, Cote Linda, Schweitzer Peter, Barba Paola, Takacs Elizabeth M, Clark Matthew, Luby James, Manns David C, Sacks Gavin, Mansfield Anna Katharine, Londo Jason, Fennell Anne, Gadoury David, Reisch Bruce, Cadle-Davidson Lance, Sun Qi (2016): A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Horticulture Research, 3, -
Zhang Shijie, Chen Weiping, Xin Lu, Gao Zhihong, Hou Yingjun, Yu Xinyi, Zhang Zhen, Qu Shenchun (2014): Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing. Horticulture Research, 1, -
Zhao Tao, Liang Dong, Wang Ping, Liu Jingying, Ma Fengwang (2012): Genome-wide analysis and expression profiling of the DREB transcription factor gene family in Malus under abiotic stress. Molecular Genetics and Genomics, 287, 423-436
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