Genotyping by Sequencing for Crop Improvement. Группа авторов
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2.2.4 Summary
SNPs constitute one of the most popular and significant genetic markers in studying disease development and progression, breeding crops for improved traits etc. Two major strategies are involved in SNP genotyping viz. allele discrimination and allele detection. The high‐throughput platforms used for SNP genotyping have generated huge amount of data in many crops. Further utilization of this information in plant breeding is important for crop improvement.
References
1 Baird, N.A., Etter, P.D., Atwood, T.S. et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3 (10): e3376.
2 Baner, J., Nilsson, M., Mendel‐Hartvig, M. et al. (1998). Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Research 26 (22): 5073–5078.
3 Bayer, M.M., Rapazote‐Flores, P., Ganal, M. et al. (2017). Development and evaluation of a barley 50k iSelect SNP array. Frontiers in Plant Science 8: 1792.
4 Bianco, L., Cestaro, A., Linsmith, G. et al. (2016). Development and validation of the Axiom® Apple480K SNP genotyping array. Plant Journal 86: 62–74. https://doi.org/10.1111/tpj.13145.
5 Branton, D., Deamer, D.W., Marziali, A. et al. (2010). The potential and challenges of nanopore sequencing. Nanoscience and Technology: A Collection of Reviews from Nature Journals: 261–268.
6 Chagné, D., Crowhurst, R.N., Troggio, M. et al. (2012). Genome‐wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 7: e31745. https://doi.org/10.1371/journal.pone.0031745.
7 Chan, M., Chan, M.W., Loh, T.W. et al. (2011). Evaluation of nanofluidics technology for highthroughput SNP genotyping in a clinical setting. The Journal of Molecular Diagnostics 13 (3): 305–312. https://doi.org/10.1016/j.jmoldx.2010.12.001.
8 Chen, X., Levine, L., and Kwok, P.Y. (1999). Fluorescence polarization in homogeneous nucleic acid analysis. Genome Research 9 (5): 492–498.
9 Eid, J., Fehr, A., Gray, J. et al. (2009). Real‐time DNA sequencing from single polymerase molecules. Science 323 (5910): 133–138.
10 Elshire, R.J., Glaubitz, J.C., Sun, Q. et al. (2011). A robust, simple genotyping‐by‐sequencing (GBS) approach for high diversity species. PLoS One 6 (5): e19379.
11 Gravel, S., Henn, B.M., Gutenkunst, R.N. et al. (2011). Demographic history and rare allele sharing among human populations. Proceedings. National Academy of Sciences. United States of America 108: 11983–11988. https://doi.org/10.1073/pnas.1019276108.
12 Kennedy, G.C., Matsuzaki, H., Dong, S. et al. (2003). Large‐scale genotyping of complex DNA. Nature Biotechnology 21: 10.
13 Khlestkin, V.K., Rozanova, I.V., Efimov, V.M. et al. (2019). Starch phosphorylation associated SNPs found by genome‐wide association studies in the potato (Solanum tuberosum L.). BMC Genetics 20 (1): 45–53.
14 Kishora, D.S., Songa, W.‐H., Noha, Y. et al. (2020). Development of SNP markers and validation assays in commercial Korean melon cultivars, using genotyping‐by‐sequencing and Fluidigm analyses. Scientia Horticulturae 263: 109113.
15 Kumar, N.M., Katageri, I.S., Gowda, S.A. et al. (2019). 63K SNP chip based linkage mapping and QTL analysis for fibre quality and yield component traits in Gossypium barbadense L. cotton. Euphytica 215 (1): 1–16.
16 LaFramboise, T. (2009). Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Research 37 (13): 4181–4193.
17 Li, Y., Haseneyer, G., Schön, C.C. et al. (2011). High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response. BMC Plant Biology 11: 6.
18 Li, X., Singh, J., Qin, M. et al. (2019). Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus). Plant Biotechnology Journal 17 (8): 1582–1594.
19 Livak, K.J. (1999). Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genetic Analysis ‐ Biomolecular Engineering 14 (5‐6): 143–149.
20 Lyamichev, V., Mast, A.L., Hall, J.G. et al. (1999). Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nature Biotechnology 17 (3): 292–296.
21 Marrano, A., Martínez‐García, P.J., Bianco, L. et al. (2019). A new genomic tool for walnut (Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array. Plant Biotechnology Journal 17 (6): 1027–1036.
22 Matsuzaki, H., Dong, S., Loi, H. et al. (2004). Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nature Biotechnology 21: 10.
23 McCouch, S.R., Wright, M.H., Tung, C.W. et al. (2016). Open access resources for genome‐wide association mapping in rice. Nature Communications 7 (1): 1–14.
24 McCouch, S.R., Wright, M.H., Tung, C.‐W. et al. (2017). Open access resources for genome‐wide association mapping in rice. Nature Communications 7: 10532. https://doi.org/10.1038/ncomms10532.
25 McCoy, R.C., Taylor, R.W., Blauwkamp, T.A. et al. (2014). Illumina TruSeq synthetic long‐reads empower de novo assembly and resolve complex, highly‐repetitive transposable elements. PLoS One 9 (9): e106689.
26 Montanari, S., Bianco, L., Allen, B.J. et al. (2019). Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high‐density mapping and germplasm characterization. BMC Genomics 20 (1): 1–18.
27 Nilsson, M., Malmgren, H., Samiotaki, M. et al. (1994). Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265 (5181): 2085–2088.
28 Oath, P., del Mistro, G., Marnellos, G. et al. (2009). Single Nucleotide Polymorphisms, Methods in Molecular Biology, vol. 578 (ed. A.A. Komar). Totowa: Humana Press Inc. https://doi.org/10.1007/978‐1‐60327‐411‐1_20.
29 Peace, C., Bassil, N., Main, D. et al. (2012). Development and evaluation of a genome‐wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One 7 (12): e48305.
30 Peng, Z., Fan, W., Wang, L. et al. (2017). Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. Molecular Genetics and Genomics 292: 955–965.