참고문헌
- Agarwal, G., Jhanwar, S., Priya, P., Singh, V.K., Saxena, M.S., Parida, S.K., Garg, R., Tyagi, A.K., and Jain, M. (2012). Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7, e52443. https://doi.org/10.1371/journal.pone.0052443
- Altshuler, D., Pollara, V.J., Cowles, C.R., Van Etten, W.J., Baldwin, J., Linton, L., and Lander, E.S. (2000). An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-516. https://doi.org/10.1038/35035083
- Barbazuk, W.B., Emrich, S.J., Chen, H.D., Li, L., and Schnable, P.S. (2007). SNP discovery via 454 transcriptome sequencing. Plant J. 51, 910-918. https://doi.org/10.1111/j.1365-313X.2007.03193.x
- Bundock, P.C., Eliott, F.G., Ablett, G., Benson, A.D., Casu, R.E., Aitken, K.S., and Henry, R.J. (2009). Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J. 7, 347-354. https://doi.org/10.1111/j.1467-7652.2009.00401.x
- Cox, M.P., Peterson, D.A., and Biggs, P.J. (2010). SolexaQA: At-aglance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11, 485. https://doi.org/10.1186/1471-2105-11-485
- Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M., and Blaxter, M.L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499-510. https://doi.org/10.1038/nrg3012
- Edwards, D., and Batley, J. (2010). Plant genome sequencing: applications for crop improvement. Plant Biotechnol. J. 8, 2-9. https://doi.org/10.1111/j.1467-7652.2009.00459.x
- Hamilton, J.P., Hansey, C.N., Whitty, B.R., Stoffel, K., Massa, A.N., Van Deynze, A., De Jong, W.S., Douches, D.S., and Buell, C.R. (2011). Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12, 302. https://doi.org/10.1186/1471-2164-12-302
- Hamilton, J.P., Sim, S.C., Stoffel, K., Van Deynze, A., Buell, C.R., and Francis, D.M. (2012). Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome 5, 17-29. https://doi.org/10.3835/plantgenome2011.12.0033
- Hyten, D.L., Cannon, S.B., Song, Q., Weeks, N., Fickus, E.W., Shoemaker, R.C., Specht, J.E., Farmer, A.D., May, G.D., and Cregan, P.B. (2010). 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, 38. https://doi.org/10.1186/1471-2164-11-38
- Li, H., and Dubin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 genome project data processing subgroup (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
-
Lu, F.H., Kwon, S.W., Yoon, M.Y., Kim, K.T., Cho, M.C., Yoon, M.K., and Park, Y.J. (2012). SNP marker integration and QTL analysis of 12 agronomic and morphological traits in
$F_8$ RILs of pepper (Capsicum annuum L.). Mol. Cells 34, 25-34. https://doi.org/10.1007/s10059-012-0018-1 - McNally, K.L., Childs, K.L., Bohnert, R., Davidson, R.M., Zhao, K., Ulat, V.J., Zeller, G., Clark, R.M., Hoen, D.R., Bureau, T.E., et al. (2009). Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA 106, 12273-12278. https://doi.org/10.1073/pnas.0900992106
- Shendure, J., and Ji, H. (2008). Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145. https://doi.org/10.1038/nbt1486
- Shirasawa, K., Isobe, S., Hirakawa, H., Asamizu, E., Fukuoka, H., Just, D., Rothan, C., Sasamoto, S., Fujishiro, T., Kishida, Y., et al. (2010). SNP discovery and linkage map construction in cultivated tomato. DNA Res. 17, 381-391. https://doi.org/10.1093/dnares/dsq024
- The Gene Ontology Consortium (2013). Gene ontology annotations and resources. Nucleic Acids Res. 41, D530-D535. https://doi.org/10.1093/nar/gks1050
- The Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641. https://doi.org/10.1038/nature11119
- Trapnell, C., Pachter, L., and Salzberg, S.L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105- 1111. https://doi.org/10.1093/bioinformatics/btp120
- Trebbi, D., Maccaferri, M., de Heer, P., Sørensen, A., Giuliani, S., Salvi, S., Sanguineti, M.C., Massi, A., van der Vossen, E.A.G., and Tuberosa, R. (2011). High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor. Appl. Genet. 123, 555-569. https://doi.org/10.1007/s00122-011-1607-7
- Trick, M., Long, Y., Meng, J., and Bancroft, I. (2009). Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol. J. 7, 334-346. https://doi.org/10.1111/j.1467-7652.2008.00396.x
피인용 문헌
- Complete genome sequencing and analysis of Capsicum annuum varieties vol.36, pp.10, 2016, https://doi.org/10.1007/s11032-016-0557-9
- Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing vol.18, pp.1, 2017, https://doi.org/10.1186/s12864-016-3406-7
- Identification of functional SNPs in genes and their effects on plant phenotypes vol.43, pp.1, 2016, https://doi.org/10.5010/JPB.2016.43.1.1
- In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits vol.12, pp.2, 2017, https://doi.org/10.1371/journal.pone.0171504
- De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa vol.39, pp.2, 2016, https://doi.org/10.14348/molcells.2016.2264
- Transcriptome Analysis of Gerbera hybrida Including in silico Confirmation of Defense Genes Found vol.7, 2016, https://doi.org/10.3389/fpls.2016.00247
- Genome-wide Single Nucleotide Polymorphism-based Assay for Phylogenetic Relationship of the Flammulina velutipes vol.43, pp.4, 2015, https://doi.org/10.4489/KJM.2015.43.4.231
- QTL mapping of resistance to the Cucumber mosaic virus P1 strain in pepper using a genotyping-by-sequencing analysis vol.57, pp.6, 2016, https://doi.org/10.1007/s13580-016-0128-3
- De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes vol.18, pp.4, 2017, https://doi.org/10.3390/ijms18040712
- Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance vol.8, pp.1, 2018, https://doi.org/10.1038/s41598-018-23279-5
- Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly vol.19, pp.1, 2018, https://doi.org/10.1186/s12864-018-4434-2
- Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing vol.293, pp.5, 2018, https://doi.org/10.1007/s00438-018-1448-z
- Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis vol.131, pp.5, 2018, https://doi.org/10.1007/s00122-018-3054-1
- Complementation of a mutation in CpSRP43 causing partial truncation of light-harvesting chlorophyll antenna in Chlorella vulgaris vol.7, pp.None, 2014, https://doi.org/10.1038/s41598-017-18221-0
- Identification of potential gene‐associated major traits using GBS‐GWAS for Korean apple germplasm collections vol.136, pp.6, 2014, https://doi.org/10.1111/pbr.12544
- Development of an efficient genotyping-by-sequencing (GBS) library construction method for genomic analysis of grapevine vol.44, pp.4, 2014, https://doi.org/10.7744/kjoas.20170061
- A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae vol.2018, pp.None, 2014, https://doi.org/10.1093/database/bay047
- De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period vol.13, pp.10, 2014, https://doi.org/10.1371/journal.pone.0205954
- Development of an Apple F1Segregating Population Genetic Linkage Map Using Genotyping-By-Sequencing vol.6, pp.4, 2014, https://doi.org/10.9787/pbb.2018.6.4.434
- Development and Application of InDel Markers for Capsicum spp. Based on Whole-Genome Re-Sequencing vol.9, pp.None, 2014, https://doi.org/10.1038/s41598-019-40244-y
- Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing vol.46, pp.4, 2014, https://doi.org/10.1007/s11033-019-04894-5
- Genotyping-by-sequencing approaches using optimized two-enzyme combinations in Asian pears (Pyrus spp.) vol.39, pp.12, 2019, https://doi.org/10.1007/s11032-019-1071-7
- Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm vol.20, pp.None, 2019, https://doi.org/10.1186/s12864-019-5645-x
- Benchmarking variant identification tools for plant diversity discovery vol.20, pp.1, 2019, https://doi.org/10.1186/s12864-019-6057-7
- Characterization of genetic variation and antioxidant properties in strawberry (Fragaria × ananassa Duch.) mutant genotypes vol.67, pp.6, 2020, https://doi.org/10.1007/s10722-020-00918-3
- Classification of Takifugu rubripes, T . chinensis and T . pseudommus by genotyping-by-sequencing vol.15, pp.8, 2014, https://doi.org/10.1371/journal.pone.0236483
- 유전자 단위 haplotype을 대변하는 토마토 Tag-SNP 선발 및 웹 데이터베이스 구축 vol.47, pp.3, 2014, https://doi.org/10.5010/jpb.2020.47.3.218
- Identification of the ‘Haryejosaeng’ mandarin cultivar by multiplex PCR-based SNP genotyping vol.47, pp.11, 2014, https://doi.org/10.1007/s11033-020-05850-4
- Improving read alignment through the generation of alternative reference via iterative strategy vol.10, pp.1, 2014, https://doi.org/10.1038/s41598-020-74526-7
- Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait vol.2021, pp.None, 2014, https://doi.org/10.1155/2021/6673010
- An Integrated Approach of QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame (Sesamum indicum L.) vol.12, pp.None, 2014, https://doi.org/10.3389/fpls.2021.604709
- Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis vol.12, pp.None, 2014, https://doi.org/10.3389/fpls.2021.752108
- Single Nucleotide Polymorphism (SNP) Discovery and Association Study of Flowering Times, Crude Fat and Fatty Acid Composition in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencin vol.11, pp.3, 2021, https://doi.org/10.3390/agronomy11030508
- Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.) vol.10, pp.11, 2021, https://doi.org/10.3390/plants10112267
- SNP-Based Genetic Linkage Map and Quantitative Trait Locus Mapping Associated with the Agronomically Important Traits of Hypsizygus marmoreus vol.49, pp.6, 2014, https://doi.org/10.1080/12298093.2021.2018784
- Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits vol.8, pp.1, 2014, https://doi.org/10.1038/s41438-021-00617-9
- Multiplex CRISPR/Cas9 Mutagenesis of BrVRN1 Delays Flowering Time in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) vol.11, pp.12, 2021, https://doi.org/10.3390/agriculture11121286
- Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon vol.11, pp.1, 2014, https://doi.org/10.3390/plants11010008