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pooled and processed simultaneously during the GBS library construction, which was checked on a Genome
Analyzer II (Illumina, Inc.). Overall, 25,185 biallelic tags were mapped in maize, while 24,186 sequence tags were mapped in barley. Barley GBS marker validation using a single DH line (OWB003) showed 99% agreement between the reference markers and the mapped GBS reads. Although barley lacks a complete genome sequence, GBS does not require a reference genome for sequence tag mapping, the reference is developed during the process of sampling genotyping. Tags can also be treated as dominant markers for alternative genetic analysis in the absence of a reference genome. Other than the multiplex GBS skimming, imputation of missing SNPs has the potential to further reduce GBS costs. GBS is a versatile and cost-effective procedure that will allow mining genomes of any species without prior knowledge of its genome structure.
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GBS is a robust, simple, and affordable procedure for SNP discovery and mapping. Overall, this approach reduces genome complexity with restriction enzymes (REs) in high-diversity, large genomes species for efficient high-throughput, highly multiplexed sequencing. By using appropriate REs, repetitive
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When initially developed, the GBS approach was tested and validated in recombinant inbred lines (RILs) from a high-resolution maize mapping population (IBM) and doubled haploid (DH) barley lines from the Oregon Wolfe Barley (OWB) mapping population. Up to 96 RE (ApeKI)-digested DNA samples were
90:. The next step is to identify SNPs from aligned tags and score all discovered SNPs for various coverage, depth and genotypic statistics. Once a large-scale, species-wide SNP production has been run, it is possible to quickly call known SNPs in newly sequenced samples.
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is performed to increase fragments pool and then GBS libraries are sequenced using next generation sequencing technologies, usually resulting in about 100bp single-end reads. It is relatively inexpensive and has been used in
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regions of genomes can be avoided and lower copy regions can be targeted, which reduces alignments problems in genetically highly diverse species. The method was first described by
Elshire et al. (2011). In summary, high
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Davey, John W.; Hohenlohe, Paul A.; Etter, Paul D.; Boone, Jason Q.; Catchen, Julian M.; Blaxter, Mark L. (2011-07-01). "Genome-wide genetic marker discovery and genotyping using next-generation sequencing".
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is performed. Next-generation sequencing technology is performed resulting in about 100 bp single-end reads. Raw sequence data are filtered and aligned to a reference genome using usually
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Heffelfinger, Christopher; Fragoso, Christopher A.; Moreno, Maria A.; Overton, John D.; Mottinger, John P.; Zhao, Hongyu; Tohme, Joe; Dellaporta, Stephen L. (2014).
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Liu, Hui; Bayer, Micha; Druka, Arnis; Russell, Joanne R.; Hackett, Christine A.; Poland, Jesse; Ramsay, Luke; Hedley, Pete E.; Waugh, Robbie (2014-01-01).
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DNAs are extracted and digested using a specific RE previously defined by cutting frequently in the major repetitive fraction of the genome.
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Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi; Poland, Jesse A.; Kawamoto, Ken; Buckler, Edward S.; Mitchell, Sharon E. (2011-05-04).
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251:"An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley"
200:"Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding"
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He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin (2014-01-01).
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Campbell, Erin O.; Brunet, Byran M.T.; Dupuis, Julian R.; Sperling, Felix A.H. (2018).
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to reduce genome complexity and genotype multiple DNA samples. After digestion,
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Vaux, Felix; Dutoit, Ludovic; Fraser, Ceridwen I.; Waters, Jonathan M. (2022).
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is the most used RE. Barcode adapters are then ligated to
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36:studies, such as genome-wide association studies (
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32:(SNP) in order to perform
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268:10.1186/1471-2164-15-104
86:alignment tool (BWA) or
22:genotyping by sequencing
399:Journal of Biogeography
379:10.1111/2041-210X.13038
311:Nature Reviews Genetics
217:10.3389/fpls.2014.00484
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110:References
34:genotyping
331:1471-0056
277:1471-2164
164:1932-6203
509:Genetics
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98:See also
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