메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Transcriptome sequencing for SNP discovery across Cucumis melo

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; TRANSCRIPTOME;

EID: 84862571155     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-280     Document Type: Article
Times cited : (84)

References (68)
  • 2
    • 84861342829 scopus 로고    scopus 로고
    • Genetic diversity studies in Cucurbits using molecular tools
    • Enfield, New Hampshire: Science Publishers Inc, Behera TK, Wang Y, Kole C
    • Esteras C, Nuez F, Picó B. Genetic diversity studies in Cucurbits using molecular tools. Genetics, Genomics and Breeding of Cucurbits 2012, 140-198. Enfield, New Hampshire: Science Publishers Inc, Behera TK, Wang Y, Kole C.
    • (2012) Genetics, Genomics and Breeding of Cucurbits , pp. 140-198
    • Esteras, C.1    Nuez, F.2    Picó, B.3
  • 3
    • 77956271593 scopus 로고    scopus 로고
    • Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia
    • 10.1073/pnas.1005338107, 2922565, 20656934
    • Sebastian P, Schaefer H, Telford IR, Renner SS. Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci 2010, 107(32):14269-14273. 10.1073/pnas.1005338107, 2922565, 20656934.
    • (2010) Proc Natl Acad Sci , vol.107 , Issue.32 , pp. 14269-14273
    • Sebastian, P.1    Schaefer, H.2    Telford, I.R.3    Renner, S.S.4
  • 6
    • 84990442853 scopus 로고
    • A review of the Cucurbitaceae
    • Jeffrey C. A review of the Cucurbitaceae. Bot J Linn Soc 1980, 81:233-247.
    • (1980) Bot J Linn Soc , vol.81 , pp. 233-247
    • Jeffrey, C.1
  • 8
    • 77953326520 scopus 로고    scopus 로고
    • Melon (Cucumis melo L.)
    • New York, USA: Springer, Prohens J, Nuez F
    • Pitrat M. Melon (Cucumis melo L.). Handbook of Crop Breeding Vol I: Vegetables 2008, 283-315. New York, USA: Springer, Prohens J, Nuez F.
    • (2008) Handbook of Crop Breeding Vol I: Vegetables , pp. 283-315
    • Pitrat, M.1
  • 9
    • 0033057580 scopus 로고    scopus 로고
    • Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation
    • Stepansky A, Kovalski I, Perl-Treves R. Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Syst Evol 1999, 217:313-333.
    • (1999) Plant Syst Evol , vol.217 , pp. 313-333
    • Stepansky, A.1    Kovalski, I.2    Perl-Treves, R.3
  • 14
    • 76749130701 scopus 로고    scopus 로고
    • High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence
    • 10.1186/1471-2164-11-38, 2817691, 20078886
    • Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 2010, 11:38. 10.1186/1471-2164-11-38, 2817691, 20078886.
    • (2010) BMC Genomics , vol.11 , pp. 38
    • Hyten, D.L.1    Cannon, S.B.2    Song, Q.3    Weeks, N.4    Fickus, E.W.5    Shoemaker, R.C.6    Specht, J.E.7    Farmer, A.D.8    May, G.D.9    Cregan, P.B.10
  • 17
    • 77952534535 scopus 로고    scopus 로고
    • Rapid genomic characterization of the genus Vitis
    • 10.1371/journal.pone.0008219, 2805708, 20084295
    • Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D. Rapid genomic characterization of the genus Vitis. PLoS One 2010, 5(1):e8219. 10.1371/journal.pone.0008219, 2805708, 20084295.
    • (2010) PLoS One , vol.5 , Issue.1
    • Myles, S.1    Chia, J.M.2    Hurwitz, B.3    Simon, C.4    Zhong, G.Y.5    Buckler, E.6    Ware, D.7
  • 18
    • 77955412222 scopus 로고    scopus 로고
    • SNP discovery by high-throughput sequencing in soybean
    • 10.1186/1471-2164-11-469, 3091665, 20701770
    • Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics 2010, 11:469. 10.1186/1471-2164-11-469, 3091665, 20701770.
    • (2010) BMC Genomics , vol.11 , pp. 469
    • Wu, X.1    Ren, C.2    Joshi, T.3    Vuong, T.4    Xu, D.5    Nguyen, H.T.6
  • 19
    • 78951478131 scopus 로고    scopus 로고
    • Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
    • 10.1186/1471-2164-12-59, 3041743, 21266061
    • You FM, Huo N, Deal KR, Gu YQ, Luo M-C, McGuire PE, Dvorak J, Anderson OD. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 2011, 12:59. 10.1186/1471-2164-12-59, 3041743, 21266061.
    • (2011) BMC Genomics , vol.12 , pp. 59
    • You, F.M.1    Huo, N.2    Deal, K.R.3    Gu, Y.Q.4    Luo, M.-C.5    McGuire, P.E.6    Dvorak, J.7    Anderson, O.D.8
  • 25
    • 79959941080 scopus 로고    scopus 로고
    • Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum
    • 10.1186/1471-2164-12-352, 3146956, 21736744
    • Nelson JC, Wang S, Wu Y, Li X, Antony G, White FF, Yu J. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics 2011, 12(1):352. 10.1186/1471-2164-12-352, 3146956, 21736744.
    • (2011) BMC Genomics , vol.12 , Issue.1 , pp. 352
    • Nelson, J.C.1    Wang, S.2    Wu, Y.3    Li, X.4    Antony, G.5    White, F.F.6    Yu, J.7
  • 26
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies the next generation
    • 10.1038/nrg2626, 19997069
    • Metzker ML. Sequencing technologies the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 27
    • 80052266118 scopus 로고    scopus 로고
    • Melon transcriptome characterization. SSRs and SNPs discovery for high throughput genotyping across the species
    • Blanca J, Cañizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, Garcia-Mas J, Picó B. Melon transcriptome characterization. SSRs and SNPs discovery for high throughput genotyping across the species. The Plant Genome 2011, 4(2):118-131.
    • (2011) The Plant Genome , vol.4 , Issue.2 , pp. 118-131
    • Blanca, J.1    Cañizares, J.2    Ziarsolo, P.3    Esteras, C.4    Mir, G.5    Nuez, F.6    Garcia-Mas, J.7    Picó, B.8
  • 30
    • 84864436441 scopus 로고    scopus 로고
    • Genetic Variations of Chinese Melon Landraces Investigated with EST-SSR Markers
    • Kong Q, Xiang C, Yang J, Yu Z. Genetic Variations of Chinese Melon Landraces Investigated with EST-SSR Markers. Hort Environ Biotechnol 2011, 52(2):163-169.
    • (2011) Hort Environ Biotechnol , vol.52 , Issue.2 , pp. 163-169
    • Kong, Q.1    Xiang, C.2    Yang, J.3    Yu, Z.4
  • 32
    • 0038334646 scopus 로고    scopus 로고
    • Genetic variability in melon based on microsatellite variation
    • Monforte AJ, Garcia-Mas J, Arús P. Genetic variability in melon based on microsatellite variation. Plant Breed 2003, 122:153-157.
    • (2003) Plant Breed , vol.122 , pp. 153-157
    • Monforte, A.J.1    Garcia-Mas, J.2    Arús, P.3
  • 34
    • 79959575830 scopus 로고    scopus 로고
    • Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
    • 10.1186/1471-2164-12-285, 3124440, 21635747
    • Blanca J, Pascual L, Ziarsolo P, Nuez F, Cañizares J. Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics 2011, 12:285. 10.1186/1471-2164-12-285, 3124440, 21635747.
    • (2011) BMC Genomics , vol.12 , pp. 285
    • Blanca, J.1    Pascual, L.2    Ziarsolo, P.3    Nuez, F.4    Cañizares, J.5
  • 35
    • 77951964897 scopus 로고    scopus 로고
    • Filtering error from SOLiD Output
    • 10.1093/bioinformatics/btq045, 20207696
    • Sasson A, Michael TP. Filtering error from SOLiD Output. Bioinformatics 2010, 26(6):849-850. 10.1093/bioinformatics/btq045, 20207696.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 849-850
    • Sasson, A.1    Michael, T.P.2
  • 36
    • 84874020286 scopus 로고    scopus 로고
    • MELONOMICS http://melonomics.upv.es.
    • MELONOMICS
  • 37
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp698, 2828108, 20080505
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 42
    • 0035651679 scopus 로고    scopus 로고
    • Genetic diversity in melon (Cucumis melo L.): An evaluation of African germplasm
    • Mliki A, Staub JE, Zhangyong S, Ghorbel A. Genetic diversity in melon (Cucumis melo L.): An evaluation of African germplasm. Genet Resour Crop Evol 2001, 48:587-597.
    • (2001) Genet Resour Crop Evol , vol.48 , pp. 587-597
    • Mliki, A.1    Staub, J.E.2    Zhangyong, S.3    Ghorbel, A.4
  • 43
    • 53249133322 scopus 로고    scopus 로고
    • Genetic diversity and phylogenetic relationship among melon accessions from Africa and Asia revealed by RAPD analysis
    • Universal Press Raleigh, Asheville, North Carolina, USA, Holmes GJ
    • Akashi Y, Tanaka K, Nishida H, Kato K, Khaning MT, Yi SS, Chou TT. Genetic diversity and phylogenetic relationship among melon accessions from Africa and Asia revealed by RAPD analysis. Proc of Cucurbitaceae 2006, 317-325. Universal Press Raleigh, Asheville, North Carolina, USA, Holmes GJ.
    • (2006) Proc of Cucurbitaceae , pp. 317-325
    • Akashi, Y.1    Tanaka, K.2    Nishida, H.3    Kato, K.4    Khaning, M.T.5    Yi, S.S.6    Chou, T.T.7
  • 44
    • 20844433441 scopus 로고    scopus 로고
    • Genetic relationship among East and South Asian melon (Cucumis melo L.) revealed by AFLP analysis
    • Yashiro K, Iwata H, Akashi Y, Tomita K, Kuzuya M, Tsumura Y, Kato K. Genetic relationship among East and South Asian melon (Cucumis melo L.) revealed by AFLP analysis. Breed Sci 2005, 55:197-206.
    • (2005) Breed Sci , vol.55 , pp. 197-206
    • Yashiro, K.1    Iwata, H.2    Akashi, Y.3    Tomita, K.4    Kuzuya, M.5    Tsumura, Y.6    Kato, K.7
  • 45
    • 33846018358 scopus 로고    scopus 로고
    • Molecular characterization of South and East Asian melon, Cucumis melo L., and the origin of Group Conomon var. makuwa and var. conomon revealed by RAPD analysis
    • Tanaka K, Nishitani A, Akashi Y, Sakata Y, Nishida H, Yoshino H, Kato K. Molecular characterization of South and East Asian melon, Cucumis melo L., and the origin of Group Conomon var. makuwa and var. conomon revealed by RAPD analysis. Euphytica 2007, 153:233-247.
    • (2007) Euphytica , vol.153 , pp. 233-247
    • Tanaka, K.1    Nishitani, A.2    Akashi, Y.3    Sakata, Y.4    Nishida, H.5    Yoshino, H.6    Kato, K.7
  • 46
    • 53249154658 scopus 로고    scopus 로고
    • Chinese melon (Cucumis melo L.) diversity analyses provide strategies for germplasm curation, genetic improvement, and evidentiary support of domestication patterns
    • Luan F, Delannay I, Staub JE. Chinese melon (Cucumis melo L.) diversity analyses provide strategies for germplasm curation, genetic improvement, and evidentiary support of domestication patterns. Euphytica 2008, 164:445-461.
    • (2008) Euphytica , vol.164 , pp. 445-461
    • Luan, F.1    Delannay, I.2    Staub, J.E.3
  • 47
    • 3242875734 scopus 로고    scopus 로고
    • Diversity among melon landraces (Cucumis melo L.) from Greece and their genetic relationships with other melon germplasm of diverse origins
    • Staub JE, López-Sesé I, Fanourakis N. Diversity among melon landraces (Cucumis melo L.) from Greece and their genetic relationships with other melon germplasm of diverse origins. Euphytica 2004, 136:151-166.
    • (2004) Euphytica , vol.136 , pp. 151-166
    • Staub, J.E.1    López-Sesé, I.2    Fanourakis, N.3
  • 49
    • 75349094365 scopus 로고    scopus 로고
    • Phenotypic and molecular diversity among landraces of snapmelon (Cucumis melo var. momordica) adapted to the hot and humid tropics of eastern India
    • Dhillon NPS, Singh J, Fergany M, Monforte AJ, Sureja AK. Phenotypic and molecular diversity among landraces of snapmelon (Cucumis melo var. momordica) adapted to the hot and humid tropics of eastern India. Plant Genetic Resources: Characterization and Utilization 2009, 7(3):291-300.
    • (2009) Plant Genetic Resources: Characterization and Utilization , vol.7 , Issue.3 , pp. 291-300
    • Dhillon, N.P.S.1    Singh, J.2    Fergany, M.3    Monforte, A.J.4    Sureja, A.K.5
  • 50
    • 70449512421 scopus 로고    scopus 로고
    • Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding
    • 10.1186/1471-2164-10-466, 2763011, 19818135
    • Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics 2009, 10:466. 10.1186/1471-2164-10-466, 2763011, 19818135.
    • (2009) BMC Genomics , vol.10 , pp. 466
    • Sim, S.C.1    Robbins, M.D.2    Chilcott, C.3    Zhu, T.4    Francis, D.M.5
  • 51
    • 77949769838 scopus 로고    scopus 로고
    • Characterization of Iranian melon landraces Groups Flexuosus and Dudaim by the analysis of morphological and Random Amplified Polymorphic DNA
    • Soltani F, Kashi A, Zamani Z, Mostofi Y, Akashi Y, Kato K. Characterization of Iranian melon landraces Groups Flexuosus and Dudaim by the analysis of morphological and Random Amplified Polymorphic DNA. Breeding Sci 2010, 60:34-45.
    • (2010) Breeding Sci , vol.60 , pp. 34-45
    • Soltani, F.1    Kashi, A.2    Zamani, Z.3    Mostofi, Y.4    Akashi, Y.5    Kato, K.6
  • 52
    • 34447513079 scopus 로고    scopus 로고
    • Evaluation of genetic diversity in Turkish melons (Cucumis melo L.) based on phenotypic characters and RAPD markers
    • Sensoy S, Buyukalaca S, Abak K. Evaluation of genetic diversity in Turkish melons (Cucumis melo L.) based on phenotypic characters and RAPD markers. Genet Resour Crop Evol 2007, 54:1351-1365.
    • (2007) Genet Resour Crop Evol , vol.54 , pp. 1351-1365
    • Sensoy, S.1    Buyukalaca, S.2    Abak, K.3
  • 53
    • 38149082678 scopus 로고    scopus 로고
    • Genetic diversity of some populations of Iranian melon using SSR markers
    • Kohpayegani JA, Behbahani M. Genetic diversity of some populations of Iranian melon using SSR markers. Biotechnology 2008, 7(1):19-26.
    • (2008) Biotechnology , vol.7 , Issue.1 , pp. 19-26
    • Kohpayegani, J.A.1    Behbahani, M.2
  • 55
    • 84879563237 scopus 로고    scopus 로고
    • Morphological characteristics and powdery mildew resistance of Cucumis melo landraces in Greece
    • Israel: International society horticultural science, Belgium, Ma'aleh Hahamisha, Katzir N, Paris HS, Acta Hort510
    • Fanourakis N, Tsekoura Z, Nanou E. Morphological characteristics and powdery mildew resistance of Cucumis melo landraces in Greece. Proc Cucurbitaceae 2000, 241-245. Israel: International society horticultural science, Belgium, Ma'aleh Hahamisha, Katzir N, Paris HS, Acta Hort510.
    • (2000) Proc Cucurbitaceae , pp. 241-245
    • Fanourakis, N.1    Tsekoura, Z.2    Nanou, E.3
  • 56
    • 44949229616 scopus 로고    scopus 로고
    • Genetic diversity in 'Carosello' and 'Barattiere' ecotypes (Cucumis melo L.)
    • Lotti C, Albo M, Ricciardi L, Conversa G, Elia A. Genetic diversity in 'Carosello' and 'Barattiere' ecotypes (Cucumis melo L.). Colture Protette 2005, N5(Suppl):44-46.
    • (2005) Colture Protette , vol.N5 , Issue.SUPPL , pp. 44-46
    • Lotti, C.1    Albo, M.2    Ricciardi, L.3    Conversa, G.4    Elia, A.5
  • 57
    • 0346038790 scopus 로고    scopus 로고
    • Genetic analysis of Spanish melon (Cucumis melo L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions
    • 10.1007/s00122-003-1404-z, 14504742
    • López-Sesé AI, Staub JE, Gómez-Guillamón ML. Genetic analysis of Spanish melon (Cucumis melo L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions. Theor Appl Genet 2003, 108(1):41-52. 10.1007/s00122-003-1404-z, 14504742.
    • (2003) Theor Appl Genet , vol.108 , Issue.1 , pp. 41-52
    • López-Sesé, A.I.1    Staub, J.E.2    Gómez-Guillamón, M.L.3
  • 59
    • 72849144274 scopus 로고    scopus 로고
    • Use of Ecotilling to identify natural allelic variants of melon candidate genes involved in fruit ripening
    • Lisbon: National Plant Genomics programmes in Europe and the European Research Area Network Plant Genomics
    • Esteras C, Pascual L, Saladie M, Dogimont C, Garcia-Mas J, Nuez F, Picó B. Use of Ecotilling to identify natural allelic variants of melon candidate genes involved in fruit ripening. 8th Plant Genomics European Meetings (Plant Gem): 7-10 October 2009 2009, 213. Lisbon: National Plant Genomics programmes in Europe and the European Research Area Network Plant Genomics.
    • (2009) 8th Plant Genomics European Meetings (Plant Gem): 7-10 October 2009 , pp. 213
    • Esteras, C.1    Pascual, L.2    Saladie, M.3    Dogimont, C.4    Garcia-Mas, J.5    Nuez, F.6    Picó, B.7
  • 60
    • 0029865316 scopus 로고    scopus 로고
    • Structure and expression of three genes encoding ACC oxidase homologs from melon (Cucumis melo L.)
    • Lasserre E, Bouquin T, Hernandez JA, Bull J, Pech JC, Balagué C. Structure and expression of three genes encoding ACC oxidase homologs from melon (Cucumis melo L.). Mol Gen Genet 1996, 251:81-90.
    • (1996) Mol Gen Genet , vol.251 , pp. 81-90
    • Lasserre, E.1    Bouquin, T.2    Hernandez, J.A.3    Bull, J.4    Pech, J.C.5    Balagué, C.6
  • 61
    • 33745589482 scopus 로고    scopus 로고
    • Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper
    • 10.1099/vir.0.81817-0, 16760413
    • Ruffel S, Gallois JL, Moury B, Robaglia C, Palloix A, Caranta C. Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper. J Gen Virol 2006, 87:2089-2098. 10.1099/vir.0.81817-0, 16760413.
    • (2006) J Gen Virol , vol.87 , pp. 2089-2098
    • Ruffel, S.1    Gallois, J.L.2    Moury, B.3    Robaglia, C.4    Palloix, A.5    Caranta, C.6
  • 64
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: predicting amino acid changes that affect protein function
    • 10.1093/nar/gkg509, 168916, 12824425
    • Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31(13):3812-3814. 10.1093/nar/gkg509, 168916, 12824425.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 67
    • 59649090821 scopus 로고    scopus 로고
    • SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform
    • Gabriel S, Ziaugra L, Tabbaa D. SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. Curr Prot Hum Genet 2009, 60(2):unit 2-12.
    • (2009) Curr Prot Hum Genet , vol.60 , Issue.2
    • Gabriel, S.1    Ziaugra, L.2    Tabbaa, D.3
  • 68
    • 18744382780 scopus 로고    scopus 로고
    • Powermarker: Integrated analysis environment for genetic marker data
    • 10.1093/bioinformatics/bti282, 15705655
    • Liu K, Muse SV. Powermarker: Integrated analysis environment for genetic marker data. Bioinformatics 2005, 21:2128-2129. 10.1093/bioinformatics/bti282, 15705655.
    • (2005) Bioinformatics , vol.21 , pp. 2128-2129
    • Liu, K.1    Muse, S.V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.