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Volumn 4, Issue 9, 2014, Pages 1681-1687

Fast and cost-effective genetic mapping in apple using next-generation sequencing

Author keywords

Apple; DNA; Genotyping bysequencing; Malus; Next generation; QTL; Sequencing; SNP

Indexed keywords

DNA; PLANT DNA;

EID: 84907916544     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.011023     Document Type: Article
Times cited : (110)

References (47)
  • 1
    • 84861363013 scopus 로고    scopus 로고
    • Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
    • Antanaviciute, L., F. Fernandez-Fernandez, J. Jansen, E. Banchi, K. Evans et al., 2012 Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genomics 13: 203.
    • (2012) BMC Genomics , vol.13 , pp. 203
    • Antanaviciute, L.1    Fernandez-Fernandez, F.2    Jansen, J.3    Banchi, E.4    Evans, K.5
  • 2
    • 54449098752 scopus 로고    scopus 로고
    • Rapid SNP discovery and genetic mapping using sequenced RAD markers
    • Baird, N. A., P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver et al., 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
    • (2008) PLoS ONE , vol.3 , pp. e3376
    • Baird, N.A.1    Etter, P.D.2    Atwood, T.S.3    Currey, M.C.4    Shiver, A.L.5
  • 3
    • 84892696295 scopus 로고    scopus 로고
    • Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map
    • Barba, P., L. Cadle-Davidson, J. Harriman, J. Glaubitz, S. Brooks et al., 2014 Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theor. Appl. Genet. 127: 73-84.
    • (2014) Theor. Appl. Genet. , vol.127 , pp. 73-84
    • Barba, P.1    Cadle-Davidson, L.2    Harriman, J.3    Glaubitz, J.4    Brooks, S.5
  • 4
    • 35748946021 scopus 로고    scopus 로고
    • TASSEL: software for association mapping of complex traits in diverse samples
    • Bradbury, P. J., Z. Zhang, D. E. Kroon, T. M. Casstevens, Y. Ramdoss et al., 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
    • (2007) Bioinformatics , vol.23 , pp. 2633-2635
    • Bradbury, P.J.1    Zhang, Z.2    Kroon, D.E.3    Casstevens, T.M.4    Ramdoss, Y.5
  • 5
  • 6
    • 0000481985 scopus 로고    scopus 로고
    • Marker-assisted selection for pest and disease resistance in the New Zealand apple breeding program
    • Bus, V., C. Ranatunga, S. Gardiner, H. Basset, E. Rikkerink et al., 2000 Marker-assisted selection for pest and disease resistance in the New Zealand apple breeding program. Acta Hortic. 538: 541-547.
    • (2000) Acta Hortic. , vol.538 , pp. 541-547
    • Bus, V.1    Ranatunga, C.2    Gardiner, S.3    Basset, H.4    Rikkerink, E.5
  • 7
    • 57349112000 scopus 로고    scopus 로고
    • Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences
    • Celton, J. M., D. S. Tustin, D. Chagné, and S. E. Gardiner, 2009 Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet. Genomes 5: 93-107.
    • (2009) Tree Genet. Genomes , vol.5 , pp. 93-107
    • Celton, J.M.1    Tustin, D.S.2    Chagné, D.3    Gardiner, S.E.4
  • 8
    • 84857433347 scopus 로고    scopus 로고
    • Genome-wide SNP detection, validation, and development of an 8K SNP array for apple
    • Chagne, D., R. N. Crowhurst, M. Troggio, M. W. Davey, B. Gilmore et al., 2012a Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7: e31745.
    • (2012) PLoS ONE , vol.7 , pp. e31745
    • Chagne, D.1    Crowhurst, R.N.2    Troggio, M.3    Davey, M.W.4    Gilmore, B.5
  • 9
    • 84856057034 scopus 로고    scopus 로고
    • QTL and candidate gene mapping for polyphenolic composition in apple fruit
    • Chagne, D., C. Krieger, M. Rassam, M. Sullivan, J. Fraser et al., 2012b QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biol. 12: 12.
    • (2012) BMC Plant Biol. , vol.12 , pp. 12
    • Chagne, D.1    Krieger, C.2    Rassam, M.3    Sullivan, M.4    Fraser, J.5
  • 10
    • 84871781068 scopus 로고    scopus 로고
    • An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes
    • Chagne, D., K. Lin-Wang, R. V. Espley, R. K. Volz, N. M. How et al., 2013 An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol. 161: 225-239.
    • (2013) Plant Physiol. , vol.161 , pp. 225-239
    • Chagne, D.1    Lin-Wang, K.2    Espley, R.V.3    Volz, R.K.4    How, N.M.5
  • 11
    • 0028151261 scopus 로고
    • Empirical threshold values for quantitative trait mapping
    • Churchill, G. A., and R. Doerge, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
    • (1994) Genetics , vol.138 , pp. 963-971
    • Churchill, G.A.1    Doerge, R.2
  • 12
    • 84870265846 scopus 로고    scopus 로고
    • A physical, genetic and functional sequence assembly of the barley genome
    • Consortium, T. I. B. G. S., 2012 A physical, genetic and functional sequence assembly of the barley genome. Nature 491: 711-716.
    • (2012) Nature , vol.491 , pp. 711-716
    • Consortium, T.I.B.G.S.1
  • 14
    • 79952479530 scopus 로고    scopus 로고
    • Application of genomics to grapevine improvement
    • di Gaspero, G., and F. Cattonaro, 2010 Application of genomics to grapevine improvement. Aust. J. Grape Wine Res. 16: 122-130.
    • (2010) Aust. J. Grape Wine Res. , vol.16 , pp. 122-130
    • di Gaspero, G.1    Cattonaro, F.2
  • 16
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto et al., 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
    • (2011) PLoS ONE , vol.6 , pp. e19379
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3    Poland, J.A.4    Kawamoto, K.5
  • 17
    • 33846404129 scopus 로고    scopus 로고
    • Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10
    • Espley, R. V., R. P. Hellens, J. Putterill, D. E. Stevenson, S. Kutty-Amma et al., 2007 Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J. 49: 414-427.
    • (2007) Plant J. , vol.49 , pp. 414-427
    • Espley, R.V.1    Hellens, R.P.2    Putterill, J.3    Stevenson, D.E.4    Kutty-Amma, S.5
  • 19
    • 80054112361 scopus 로고    scopus 로고
    • Integration of physical and genetic maps in apple confirms wholegenome and segmental duplications in the apple genome
    • Han, Y., D. Zheng, S. Vimolmangkang, M. A. Khan, J. E. Beever et al., 2011 Integration of physical and genetic maps in apple confirms wholegenome and segmental duplications in the apple genome. J. Exp. Bot. 62: 5117-5130
    • (2011) J. Exp. Bot. , vol.62 , pp. 5117-5130
    • Han, Y.1    Zheng, D.2    Vimolmangkang, S.3    Khan, M.A.4    Beever, J.E.5
  • 21
    • 15044363993 scopus 로고    scopus 로고
    • Genetic linkage maps of two apple cultivars (Malus × domestica Borkh.) based on AFLP and microsatellite markers
    • Kenis, K., and J. Keulemans, 2005 Genetic linkage maps of two apple cultivars (Malus × domestica Borkh.) based on AFLP and microsatellite markers. Mol. Breed. 15: 205-219.
    • (2005) Mol. Breed. , vol.15 , pp. 205-219
    • Kenis, K.1    Keulemans, J.2
  • 22
    • 84868353666 scopus 로고    scopus 로고
    • A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome
    • Khan, M. A., Y. Han, Y. F. Zhao, M. Troggio, and S. S. Korban, 2012 A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS ONE 7: e47864.
    • (2012) PLoS ONE , vol.7 , pp. e47864
    • Khan, M.A.1    Han, Y.2    Zhao, Y.F.3    Troggio, M.4    Korban, S.S.5
  • 23
    • 84860503096 scopus 로고    scopus 로고
    • Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.)
    • Kumar, S., D. Chagné, M. C. A. M. Bink, R. K. Volz, C. Whitworth et al., 2012 Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.). PLoS ONE 7: e36674.
    • (2012) PLoS ONE , vol.7 , pp. e36674
    • Kumar, S.1    Chagné, D.2    Bink, M.C.A.M.3    Volz, R.K.4    Whitworth, C.5
  • 24
    • 84878814495 scopus 로고    scopus 로고
    • Novel genomic approaches unravel genetic architecture of complex traits in apple
    • Kumar, S., D. Garrick, M. Bink, C. Whitworth, D. Chagne et al., 2013 Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14: 393.
    • (2013) BMC Genomics , vol.14 , pp. 393
    • Kumar, S.1    Garrick, D.2    Bink, M.3    Whitworth, C.4    Chagne, D.5
  • 25
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 28
    • 79958703058 scopus 로고    scopus 로고
    • High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex
    • Lin-Wang, K. U. I., D. Micheletti, J. Palmer, R. Volz, L. Lozano et al., 2011 High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex. Plant Cell Environ. 34: 1176-1190.
    • (2011) Plant Cell Environ. , vol.34 , pp. 1176-1190
    • Lin-Wang, K.U.I.1    Micheletti, D.2    Palmer, J.3    Volz, R.4    Lozano, L.5
  • 29
    • 84873505245 scopus 로고    scopus 로고
    • Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol
    • Lu, F., A. E. Lipka, J. Glaubitz, R. Elshire, J. H. Cherney et al., 2013 Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol. PLoS Genet. 9: e1003215.
    • (2013) PLoS Genet. , vol.9 , pp. e1003215
    • Lu, F.1    Lipka, A.E.2    Glaubitz, J.3    Elshire, R.4    Cherney, J.H.5
  • 30
    • 84886793453 scopus 로고    scopus 로고
    • Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
    • Mascher, M., G. J. Muehlbauer, D. S. Rokhsar, J. Chapman, J. Schmutz et al., 2013a Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76: 718-727.
    • (2013) Plant J. , vol.76 , pp. 718-727
    • Mascher, M.1    Muehlbauer, G.J.2    Rokhsar, D.S.3    Chapman, J.4    Schmutz, J.5
  • 31
    • 84884835056 scopus 로고    scopus 로고
    • Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley
    • Mascher, M., S. Wu, P. S. Amand, N. Stein, and J. Poland, 2013b Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8: e76925.
    • (2013) PLoS ONE , vol.8 , pp. e76925
    • Mascher, M.1    Wu, S.2    Amand, P.S.3    Stein, N.4    Poland, J.5
  • 32
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data
    • McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., 2010 The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Res. 20: 1297-1303.
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5
  • 33
    • 79960589122 scopus 로고    scopus 로고
    • Genetic diversity of the genus Malus and implications for linkage mapping with SNPs
    • Micheletti, D., M. Troggio, A. Zharkikh, F. Costa, M. Malnoy et al., 2011 Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet. Genomes 7: 857.
    • (2011) Tree Genet. Genomes , vol.7 , pp. 857
    • Micheletti, D.1    Troggio, M.2    Zharkikh, A.3    Costa, F.4    Malnoy, M.5
  • 34
    • 84893580899 scopus 로고    scopus 로고
    • Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls
    • (submitted).
    • Miller, A., N. Matasci, M. K. Aradhya, B. H. Prins, G. Y. Zhong et al., 2013 Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS ONE (submitted).
    • (2013) PLoS ONE
    • Miller, A.1    Matasci, N.2    Aradhya, M.K.3    Prins, B.H.4    Zhong, G.Y.5
  • 35
    • 84880513155 scopus 로고    scopus 로고
    • Improving fruit and wine: what does genomics have to offer?
    • Myles, S., 2013 Improving fruit and wine: what does genomics have to offer? Trends Genet. 29: 190-196.
    • (2013) Trends Genet. , vol.29 , pp. 190-196
    • Myles, S.1
  • 36
    • 84875444971 scopus 로고    scopus 로고
    • Genotyping-by-sequencing for plant breeding and genetics
    • Poland, J. A., and T. W. Rife, 2012 Genotyping-by-sequencing for plant breeding and genetics. Plant Gen. 5: 92-102.
    • (2012) Plant Gen. , vol.5 , pp. 92-102
    • Poland, J.A.1    Rife, T.W.2
  • 38
    • 84857520461 scopus 로고    scopus 로고
    • Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach
    • Poland, J. A., P. J. Brown, M. E. Sorrells, and J.-L. Jannink, 2012b Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7: e32253.
    • (2012) PLoS ONE , vol.7 , pp. e32253
    • Poland, J.A.1    Brown, P.J.2    Sorrells, M.E.3    Jannink, J.-L.4
  • 39
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: A tool set for whole-genome association and populationbased linkage analyses
    • Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira et al., 2007 PLINK: A tool set for whole-genome association and populationbased linkage analyses. Am. J. Hum. Genet. 81: 559-575.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 559-575
    • Purcell, S.1    Neale, B.2    Todd-Brown, K.3    Thomas, L.4    Ferreira, M.A.R.5
  • 40
    • 84878685948 scopus 로고    scopus 로고
    • Comprehensive genotyping of the USA national maize inbred seed bank
    • Romay, M., M. Millard, J. Glaubitz, J. Peiffer, K. Swarts et al., 2013 Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 14: R55.
    • (2013) Genome Biol. , vol.14 , pp. R55
    • Romay, M.1    Millard, M.2    Glaubitz, J.3    Peiffer, J.4    Swarts, K.5
  • 41
    • 84872789979 scopus 로고    scopus 로고
    • An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping
    • Sonah, H., M. Bastien, E. Iquira, A. Tardivel, G. Légaré et al., 2013 An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8: e54603.
    • (2013) PLoS ONE , vol.8 , pp. e54603
    • Sonah, H.1    Bastien, M.2    Iquira, E.3    Tardivel, A.4    Légaré, G.5
  • 42
    • 84887613153 scopus 로고    scopus 로고
    • Bridging the genotyping gap: using genotyping by sequencing (GBS) to add highdensity SNP markers and new value to traditional bi-parental mapping and breeding populations
    • Spindel, J., M. Wright, C. Chen, J. Cobb, J. Gage et al., 2013 Bridging the genotyping gap: using genotyping by sequencing (GBS) to add highdensity SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor. Appl. Genet. 126: 2699-2716.
    • (2013) Theor. Appl. Genet. , vol.126 , pp. 2699-2716
    • Spindel, J.1    Wright, M.2    Chen, C.3    Cobb, J.4    Gage, J.5
  • 43
    • 7344254829 scopus 로고
    • Construction of integrated genetic linkage maps by means of a new computer package: JoinMap
    • Stam, P., 1993 Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 5: 739-744.
    • (1993) Plant J. , vol.5 , pp. 739-744
    • Stam, P.1
  • 44
    • 33751085875 scopus 로고    scopus 로고
    • Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples
    • Takos, A. M., F. W. Jaffé, S. R. Jacob, J. Bogs, S. P. Robinson et al., 2006 Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol. 142: 1216-1232.
    • (2006) Plant Physiol. , vol.142 , pp. 1216-1232
    • Takos, A.M.1    Jaffé, F.W.2    Jacob, S.R.3    Bogs, J.4    Robinson, S.P.5
  • 46
    • 84872191379 scopus 로고    scopus 로고
    • Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation
    • Ward, J., J. Bhangoo, F. Fernandez-Fernandez, P. Moore, J. Swanson et al., 2013 Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14: 2.
    • (2013) BMC Genomics , vol.14 , pp. 2
    • Ward, J.1    Bhangoo, J.2    Fernandez-Fernandez, F.3    Moore, P.4    Swanson, J.5
  • 47
    • 79958722074 scopus 로고    scopus 로고
    • Utility testing of an apple skin color MdMYB1 marker in two progenies
    • Zhu, Y., K. Evans, and C. Peace, 2011 Utility testing of an apple skin color MdMYB1 marker in two progenies. Mol. Breed. 27: 525-532.
    • (2011) Mol. Breed. , vol.27 , pp. 525-532
    • Zhu, Y.1    Evans, K.2    Peace, C.3


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