Identification of functional SNPs in genes and their effects on plant phenotypes

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참고문헌 (101)

1. Akond M, "A SNP-based genetic linkage map of soybean using the SoySNP6K illumina infinium beadchip genotyping array", Journal of Plant Genome Sciences, 1, pp.80~89 (2013)
2. Alexandra M, "Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)", Plant Biotechnol J, 9, pp.1086~1099 (2011)
3. Alkan C, "Genome structural variation discovery and genotyping", Nat Rev Genet, 12, pp.363~376 (2011)
4. Allen AM, "Transcriptspecific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)", Plant Biotechnol J, 9, pp.1086~1099 (2011)
5. Aranzana MJ, "Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes", PLoS Genet, 1, pp.e60~ (2005)
6. Barchi L, "Identification of SNP and SSR markers in eggplant using RAD tag sequencing", BMC Genomics, 12, pp.304~ (2011)
7. Buckler ES, "The genetic architecture of maize flowering time", Science, 325, pp.714~718 (2009)
8. Byers RL, "Development and mapping of SNP assays in allotetraploid cotton", Theor Appl Genet, 124, pp.1201~1214 (2012)
9. Causse M, "Whole genome resequencing in tomato reveals variation associated with introgression and breeding events", BMC Genomics, 14, pp.791~ (2013)
10. Chen H, "A high-density SNP genotyping array for rice biology and molecular breeding", Mol Plant, 7, pp.541~553 (2014)
11. Ching A, "SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines", BMC Genet, 3, pp.19~ (2002)
12. Chung WH, "Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes", DNA Research, 21, pp.153~167 (2014)
13. Clark SE, "Effects of single nucleotide polymorphisms in β-amylase1 alleles from barley on functional properties of the enzymes", Plant Physiol Bioch, 41, pp.798~804 (2003)
14. Cort´es AJ, "SNP marker diversity in common bean (Phaseolus vulgaris L.)", Theor Appl Genet, 123, pp.827~845 (2011)
15. Davey JW, "Genome-wide genetic marker discovery and genotyping using next-generation sequencing", Nat Rev Genet, 12, pp.499~510 (2011)
16. Dubcovsky, J., "Genome plasticity: a key factor in the success of polyploid wheat under domestication", Science, 316, pp.1862~1866 (2007)
17. Elshire RJ, "A robust, simple genotyping-bysequencing (GBS) approach for high diversity species", PLoS ONE, 6, pp.e19379~ (2011)
18. Fridman E, "Zooming in on a quantitative trait for tomato yield using interspecific introgressions", Science, 305, pp.1786~1789 (2004)
19. Fu YB, "Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing", Genet Resour Crop Evol, 61, pp.579~594 (2014)
20. Fu YB, "Genetic diversity analysis with 454pyrosequencing and genomic reduction confirmed the eastern and western division in the cultivated barley gene pool", Plant Genome, 4, pp.226~237 (2011)
21. Ganal MW, "SNP identification in crop plants", Curr Opin Plant Biol, 12, pp.211~217 (2009)
22. Goff SA, "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)", Science, 296, pp.92~100 (2002)
23. Gut IG, "Automation in genotyping of single nucleotide polymorphisms", Hum Mutat, 17, pp.475~492 (2001)
24. Hamilton JP, "Single nucleotide polymorphism discovery in elite north american potato germplasm", BMC Genomics, 12, pp.302~ (2011)
25. Hamilton JP, "Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis", Plant Genome, 5, pp.17~29 (2012)
26. Hirakawa H, "Draft genome sequence of eggplant (Solanum melongena L.): the representative Solanum species indigenous to the old world", DNA Res, 2, pp.649~660 (2014)
27. Hirakawa H, "Genome-wide SNP genotyping to infer the effects on gene functions in tomato", DNA Res, 20, pp.221~233 (2013)
28. Hont AD, "The banana (Musa acuminata) genome and the evolution of monocotyledonous plants", Nature, 488, pp.213~217 (2012)
29. Huang S, "The genome of the cucumber, Cucumis sativus L", Nat Genet, 41, pp.1275~1281 (2009)
30. Huang X, "High-throughput genotyping by whole-genome resequencing", Genome Res, 19, pp.1068~1076 (2009)
31. Huang X, "Genome-wide association studies of 14agronomic traits in rice landraces", Nat Genet, 42, pp.961~967 (2010)
32. Md. Amdadul Huq, "Genome Sequencing, a Milestone for Genomic Research and Plant Breeding", Plant Breeding and Biotechnology, 4(1), pp.29~39 (2016), 한국육종학회[DOI]
33. Hyten DL, "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, 11, pp.38~ (2010)
34. International Rice Genome Sequencing Project, "The map-based sequence of the rice genome", Nature, 436, pp.793~800 (2005)
35. Jang SJ, "A single-nucleotide polymorphism in an endo-1,4-β-glucanase gene controls seed coat permeability in soybean", Plos One, 10, pp.e0128527~ (2015)
36. Jeong IS, "SNP-based analysis of genetic diversity in anther derived rice by whole genome sequencing", Rice, 6, pp.6~ (2013)[DOI]
37. Jones E, "Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm", Mol Breeding, 24, pp.165~176 (2009)
38. Kharabian-Masouleh A, "SNP in starch biosynthesis genes associated with nutritional and functional properties of rice", Sci Rep, 2, pp.557~ (2012)
39. Ji-Eun Kim, "Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato", Molecules and Cells, 37(1), pp.36~42 (2014), 한국분자세포생물학회
40. Kircher M, "High-throughput DNA sequencing. concepts and limitations", BioEssays, 32, pp.524~536 (2010)
41. Kruglyak L, "The use of a genetic map of biallelic markers in linkage studies", Nat Genet, 17, pp.21~24 (1997)
42. Kumar B, "Association analysis of single nucleotide polymorphisms in candidate genes with root traits in maize (Zea mays L.) seedlings", Plant Science, 224, pp.9~19 (2014)
43. Kumar S, "SNP discovery through next-generation sequencing and its applications", Int J Plant Genomics, 2012, pp.831460~ (2012)[DOI]
44. Lam HM, "Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection", Nat Genet, 42, pp.1053~1059 (2010)
45. Lee YG, "Development, validation and genetic analysis of a large soybean SNP genotyping array", Plant J, 81, pp.625~636 (2015)
46. LeVan TD, "A common single nucleotide polymorphism in the CD 14 promoter decreases the affinity of Sp protein binding and enhances transcriptional activity", J Immunol, 167, pp.5838~5844 (2001)
47. Li F, "A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits", DNA Res, 16, pp.311~323 (2009)
48. Lu F, "Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol", PLoS Genet, 9, pp.e1003215~ (2013)
49. Mardis ER, "The impact of next-generation sequencing technology on genetics", Trends Genet, 24, pp.133~141 (2007)
50. Mayer KF, "A physical, genetic and functional sequence assembly of the barley genome", Nature, 491, pp.711~716 (2012)
51. McCouch SR, "Development of genome-wide SNP assays for rice", Breed Sci, 60, pp.524~535 (2010)
52. McNally KL, "Genomewide SNP variation reveals relationships among landraces and modern varieties of rice", Proc Natl Acad Sci USA, 106, pp.12273~12278 (2009)
53. Morin PA, "SNPs in ecology, evolution and conservation", Trends in Ecology and Evolution, 19, pp.208~216 (2004)
54. Muraya MM, "Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition", PLoS One, 10, pp.e0132120~ (2015)
55. Oliver RE, "Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology", BMC Genomics, 12, pp.77~ (2011)
56. Pajerowska-Mukhtar K, "Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars", Genetics, 181, pp.1115~1127 (2009)
57. Parida SK, "SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure", BMC Genomics, 13, pp.426~ (2012)
58. Pasam RK, "Genome-wide association studies for agronomical traits in a world-wide spring barley collection", BMC Plant Biology, 12, pp.16~ (2012)
59. Poland J, "Genomic selection in wheat breeding using genotyping-by-sequencing", Plant Genome, 5, pp.103~113 (2012)
60. Poland JA, "Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize", Proc Natl Acad Sci USA, 108, pp.6893~6898 (2011)
61. Poland JA, "Genotyping-by-sequencing for plant breeding and genetics", Plant Genome, 5, pp.92~102 (2012)
62. Potato Genome Sequencing Consortium, "Genome sequence and analysis of the tuber crop potato", Nature, 475, pp.189~195 (2011)
63. Rafalski A, "Applications of single nucleotide polymorphisms in crop genetics", Curr Opin Plant Biol, 5, pp.94~100 (2002)
64. Rostoks N, "Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress", Mol Genet Genomics, 274, pp.515~527 (2005)
65. Sachidanandam R, "A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms", Nature, 409, pp.928~933 (2001)
66. Sanger F, "DNA sequencing with chain-terminating inhibitors", Proc Natl Acad Sci USA, 74, pp.5463~5467 (1977)
67. Sanger F, "Nucleotide sequence of bacteriophage phiX174 DNA", Nature, 265, pp.687~695 (1977)
68. Schmutz J, "Genome sequence of the palaeopolyploid soybean", Nature, 463, pp.178~183 (2010)
69. Schnable PS, "The B73 maize genome: complexity, diversity, and dynamics", Science, 326, pp.1112~1115 (2009)
70. Schreiber L, "SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.)", G3 (Bethesda), 4, pp.1797~1811 (2014)
71. Shi Z, "SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance", BMC Genomics, 16, pp.314~ (2015)
72. Shirasawa K, "Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato", DNA Res, 20, pp.593~603 (2013)
73. Shirasawa K, "Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato", Plant Biotechnol J, 14, pp.51~60 (2016)
74. Singh R, "Oil palm genome sequence reveals divergence of interfertile species in old and new worlds", Nature, 500, pp.335~339 (2013)
75. Sonah H, "An improved genotyping by sequencing (GBS) approach offering increased ver-satility and efficiency of SNP discovery and genotyping", PLoS One, 8, pp.e54603~ (2013)
76. Song Q, "Development and evaluation of SoySNP50K, a high-density genotyping array for soybean", PLoS One, 8, pp.e54985~ (2013)
77. Spindel J, "Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations", Theor Appl Genet, 126, pp.2699~2716 (2013)
78. Steemers FJ, "Whole genome genotyping technologies on the bead array platform", Biotechnol J, 2, pp.41~49 (2007)
79. Sun R, "A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality", BMC Genomics, 16, pp.747~ (2015)
80. Tenaillon MI, "Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)", Proc Natl Acad Sci USA, 98, pp.9161~9166 (2001)
81. The 100 Tomato Genome Sequencing Consortium, "Exploring genetic variation in the tomato (Solanum section Lycopersicon)clade by whole-genome sequencing", Plant J, 80, pp.136~148 (2014)
82. Tomato Genome Consortium, "The tomato genome sequence provides insights into fleshy fruit evolution", Nature, 485, pp.635~641 (2012)
83. Truong HT, "Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations", PLoS One, 7, pp.e37565~ (2012)
84. Tung CW, "Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)", Rice, 3, pp.205~217 (2010)
85. Uitdewilligen JG, "A next-generation sequencing method for genotyping by-sequencing of highly heterozygous autotetraploid potato", PLoS ONE, 8, pp.e62355~ (2013)
86. Velasco R, "The genome of the domesticated apple (Malus x domestica Borkh.)", Nat Genet, 42, pp.833~839 (2010)
87. Velasco R, "A high quality draft consensus sequence of the genome of a heterozygous grapevine variety", PLoS One, 2, pp.e1326~ (2007)
88. Vidal RO, "Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance", Genet Mol Biol, 35, pp.331~334 (2012)
89. Vignal A, "A review on SNP and other types of molecular markers and their use in animal genetics", Genet Sel Evol, 34, pp.275~305 (2002)
90. Wang S, "Characterization of polyploid wheat genomic diversity using a high-density 90000single nucleotide polymorphism array", Plant Biotechnol J, 12, pp.787~796 (2014)
91. Waugh R, "The emergence of whole genome association scans in barley", Curr Opin Plant Biol, 12, pp.218~222 (2009)
92. Wei O, "Nucleotide diversity and molecular evolution of the WAG-2gene in common wheat (Triticum aestivum L.) and its relatives", Genet Mol Biol, 34, pp.606~615 (2011)
93. Wei Q, "An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing", BMC Genomics, 15, pp.1158~ (2014)
94. Xia Y, "Single nucleotide polymorphisms in HSP17.8 and their association with agronomic traits in barley", PLoS One, 8, pp.e56816~ (2013)
95. Xie W, "Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing", Proc Natl Acad Sci USA, 107, pp.10578~10583 (2010)
96. Xu J, "Identification of candidate genes for drought tolerance by whole-genome resequencing in maize", BMC Plant Biology, 14, pp.83~ (2014)
97. Yu H, "A whole-genome SNP array (RICE6K) for genomic breeding in rice", Plant Biotechnol J, 12, pp.28~37 (2014)
98. Yu J, "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)", Science, 296, pp.79~92 (2002)
99. Zhang X, "Global analysis of allele-specific expression in Arabidopsis thaliana", Genetics, 182, pp.943~954 (2009)
100. Zhao K, "Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa", Nat Commun, 2, pp.467~ (2011)
101. Zhou Z, "Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean", Nature Biotechnology, 33, pp.408~414 (2015)

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