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In the field of [[DNA sequencing|genetic sequencing]], '''genotyping by sequencing''', also called '''GBS''', is a method to discover [[Single-nucleotide polymorphism|single nucleotide polymorphisms]] (SNP) in order to perform [[genotyping]] studies, such as genome-wide association studies ([[Genome-wide association study|GWAS]]).<ref name=":1">{{Cite journal|last1=Elshire|first1=Robert J.|last2=Glaubitz|first2=Jeffrey C.|last3=Sun|first3=Qi|last4=Poland|first4=Jesse A.|last5=Kawamoto|first5=Ken|last6=Buckler|first6=Edward S.|last7=Mitchell|first7=Sharon E.|date=2011-05-04|title=A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species|journal=PLOS ONE|volume=6|issue=5|article-number=e19379|doi=10.1371/journal.pone.0019379|issn=1932-6203|pmc=3087801|pmid=21573248|bibcode=2011PLoSO...619379E|doi-access=free}}</ref> GBS uses [[restriction enzyme]]s to reduce genome complexity and genotype multiple DNA samples.<ref name=":0">{{Cite journal|last1=He|first1=Jiangfeng|last2=Zhao|first2=Xiaoqing|last3=Laroche|first3=André|last4=Lu|first4=Zhen-Xiang|last5=Liu|first5=HongKui|last6=Li|first6=Ziqin|date=2014-01-01|title=Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding|journal= Frontiers in Plant Science|volume=5|page=484|doi=10.3389/fpls.2014.00484|pmc=4179701|pmid=25324846|doi-access=free}}</ref> After digestion, [[Polymerase chain reaction|PCR]] 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.<ref>{{Cite journal|last1=Liu|first1=Hui|last2=Bayer|first2=Micha|last3=Druka|first3=Arnis|last4=Russell|first4=Joanne R.|last5=Hackett|first5=Christine A.|last6=Poland|first6=Jesse|last7=Ramsay|first7=Luke|last8=Hedley|first8=Pete E.|last9=Waugh|first9=Robbie|date=2014-01-01|title=An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley|journal=BMC Genomics|volume=15|page=104|doi=10.1186/1471-2164-15-104|issn=1471-2164|pmc=3922333|pmid=24498911 |doi-access=free }}</ref> It is relatively inexpensive and has been used in [[plant breeding]].<ref name=":0" /> Although GBS presents an approach similar to [[Restriction site associated DNA markers|restriction-site-associated DNA sequencing]] (RAD-seq) method, they differ in some substantial ways.<ref>{{Cite journal|last1=Davey|first1=John W.|last2=Hohenlohe|first2=Paul A.|last3=Etter|first3=Paul D.|last4=Boone|first4=Jason Q.|last5=Catchen|first5=Julian M.|last6=Blaxter|first6=Mark L.|date=2011-07-01|title=Genome-wide genetic marker discovery and genotyping using next-generation sequencing|journal=Nature Reviews Genetics|language=en|volume=12|issue=7|pages=499–510|doi=10.1038/nrg3012|pmid=21681211|s2cid=15080731|issn=1471-0056}}</ref><ref name="Campbell-2018">{{cite journal |doi=10.1111/2041-210X.13038 |title=Would an RRS by any other name sound as RAD? |journal=Methods in Ecology and Evolution |volume=9 |issue=9 |pages=1920–1927 |year=2018 |last1=Campbell|first1=Erin O. |last2=Brunet|first2=Byran M.T. |last3=Dupuis|first3=Julian R. |last4=Sperling|first4=Felix A.H.|doi-access=free}}</ref><ref name="Vaux-2023">{{cite journal |doi=10.1111/jbi.14516 |title=Genotyping-by-sequencing for biogeography |journal=Journal of Biogeography |volume= 50|issue= 2|pages= 262–281|year=2022 |last1=Vaux|first1=Felix |last2=Dutoit|first2=Ludovic |last3=Fraser|first3=Ceridwen I. |last4=Waters|first4=Jonathan M.|doi-access=free}}</ref>

== Methods ==
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 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).<ref name=":1" /> In summary, high [[Molecular mass|molecular weight]] DNAs are extracted and digested using a specific RE previously defined by cutting frequently<ref>{{Cite journal | doi=10.1186/1471-2164-15-979| pmid=25406744| pmc=4253001|title = Flexible and scalable genotyping-by-sequencing strategies for population studies| journal=BMC Genomics| volume=15| page=979|year = 2014|last1 = Heffelfinger|first1 = Christopher| last2=Fragoso| first2=Christopher A.| last3=Moreno| first3=Maria A.| last4=Overton| first4=John D.| last5=Mottinger| first5=John P.| last6=Zhao| first6=Hongyu| last7=Tohme| first7=Joe| last8=Dellaporta| first8=Stephen L.| issue=1| doi-access=free }}</ref> in the major repetitive fraction of the genome. ''ApeKI'' is the most used RE. Barcode adapters are then ligated to [[Sticky and blunt ends|sticky ends]] and [[Polymerase chain reaction|PCR amplification]] 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 [[Burrows–Wheeler Aligner|Burrows–Wheeler]] alignment tool (BWA) or [[Bowtie (sequence analysis)|Bowtie 2]]. 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.<ref>{{cite web|url=https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline|title=Tassel 5 GBS v2 Pipeline|website=Tassel 5 Source|access-date=20 May 2016}}</ref>

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 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.<ref name=":1" />

==See also==
*[[Restriction site associated DNA markers]]

==References==
{{Reflist}}

[[Category:Genetics]]
[[Category:Biotechnology]]
[[Category:DNA sequencing]]

Genotyping by sequencing - История изменений

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ru>Trappist the monk: cite repair (Category:CS1 maint: article number as page number);