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Genotyping by sequencing

January 01, 1970

In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies (GWAS).[1] GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples.[2] After digestion, 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.[3] It is relatively inexpensive and has been used in plant breeding.[2] Although GBS presents an approach similar to restriction-site-associated DNA sequencing (RAD-seq) method, they differ in some substantial ways.[4][5][6]

Methods edit

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).[1] In summary, high molecular weight DNAs are extracted and digested using a specific RE previously defined by cutting frequently[7] in the major repetitive fraction of the genome. ApeKI is the most used RE. Barcode adapters are then ligated to sticky ends and 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 alignment tool (BWA) or 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.[8]

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. [1]

See also edit

References edit

  1. ^ a b c Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi; Poland, Jesse A.; Kawamoto, Ken; Buckler, Edward S.; Mitchell, Sharon E. (2011-05-04). "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species". PLOS ONE. 6 (5): e19379. Bibcode:2011PLoSO...619379E. doi:10.1371/journal.pone.0019379. ISSN 1932-6203. PMC 3087801. PMID 21573248.
  2. ^ a b He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin (2014-01-01). "Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding". Frontiers in Plant Science. 5: 484. doi:10.3389/fpls.2014.00484. PMC 4179701. PMID 25324846.
  3. ^ Liu, Hui; Bayer, Micha; Druka, Arnis; Russell, Joanne R.; Hackett, Christine A.; Poland, Jesse; Ramsay, Luke; Hedley, Pete E.; Waugh, Robbie (2014-01-01). "An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley". BMC Genomics. 15: 104. doi:10.1186/1471-2164-15-104. ISSN 1471-2164. PMC 3922333. PMID 24498911.
  4. ^ 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". Nature Reviews Genetics. 12 (7): 499–510. doi:10.1038/nrg3012. ISSN 1471-0056. PMID 21681211. S2CID 15080731.
  5. ^ Campbell, Erin O.; Brunet, Byran M.T.; Dupuis, Julian R.; Sperling, Felix A.H. (2018). "Would an RRS by any other name sound as RAD?". Methods in Ecology and Evolution. 9 (9): 1920–1927. doi:10.1111/2041-210X.13038.
  6. ^ Vaux, Felix; Dutoit, Ludovic; Fraser, Ceridwen I.; Waters, Jonathan M. (2022). "Genotyping-by-sequencing for biogeography". Journal of Biogeography. 50 (2): 262–281. doi:10.1111/jbi.14516.
  7. ^ Heffelfinger, Christopher; Fragoso, Christopher A.; Moreno, Maria A.; Overton, John D.; Mottinger, John P.; Zhao, Hongyu; Tohme, Joe; Dellaporta, Stephen L. (2014). "Flexible and scalable genotyping-by-sequencing strategies for population studies". BMC Genomics. 15 (1): 979. doi:10.1186/1471-2164-15-979. PMC 4253001. PMID 25406744.
  8. ^ "Tassel 5 GBS v2 Pipeline". Tassel 5 Source. Retrieved 20 May 2016.

January 01, 1970
genotyping, sequencing, field, genetic, sequencing, genotyping, sequencing, also, called, method, discover, single, nucleotide, polymorphisms, order, perform, genotyping, studies, such, genome, wide, association, studies, gwas, uses, restriction, enzymes, redu. In the field of genetic sequencing genotyping by sequencing also called GBS is a method to discover single nucleotide polymorphisms SNP in order to perform genotyping studies such as genome wide association studies GWAS 1 GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples 2 After digestion 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 3 It is relatively inexpensive and has been used in plant breeding 2 Although GBS presents an approach similar to restriction site associated DNA sequencing RAD seq method they differ in some substantial ways 4 5 6 Methods editGBS 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 1 In summary high molecular weight DNAs are extracted and digested using a specific RE previously defined by cutting frequently 7 in the major repetitive fraction of the genome ApeKI is the most used RE Barcode adapters are then ligated to sticky ends and 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 alignment tool BWA or 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 8 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 1 See also editRestriction site associated DNA markersReferences edit a b c Elshire Robert J Glaubitz Jeffrey C Sun Qi Poland Jesse A Kawamoto Ken Buckler Edward S Mitchell Sharon E 2011 05 04 A Robust Simple Genotyping by Sequencing GBS Approach for High Diversity Species PLOS ONE 6 5 e19379 Bibcode 2011PLoSO 619379E doi 10 1371 journal pone 0019379 ISSN 1932 6203 PMC 3087801 PMID 21573248 a b He Jiangfeng Zhao Xiaoqing Laroche Andre Lu Zhen Xiang Liu HongKui Li Ziqin 2014 01 01 Genotyping by sequencing GBS an ultimate marker assisted selection MAS tool to accelerate plant breeding Frontiers in Plant Science 5 484 doi 10 3389 fpls 2014 00484 PMC 4179701 PMID 25324846 Liu Hui Bayer Micha Druka Arnis Russell Joanne R Hackett Christine A Poland Jesse Ramsay Luke Hedley Pete E Waugh Robbie 2014 01 01 An evaluation of genotyping by sequencing GBS to map the Breviaristatum e ari e locus in cultivated barley BMC Genomics 15 104 doi 10 1186 1471 2164 15 104 ISSN 1471 2164 PMC 3922333 PMID 24498911 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 Nature Reviews Genetics 12 7 499 510 doi 10 1038 nrg3012 ISSN 1471 0056 PMID 21681211 S2CID 15080731 Campbell Erin O Brunet Byran M T Dupuis Julian R Sperling Felix A H 2018 Would an RRS by any other name sound as RAD Methods in Ecology and Evolution 9 9 1920 1927 doi 10 1111 2041 210X 13038 Vaux Felix Dutoit Ludovic Fraser Ceridwen I Waters Jonathan M 2022 Genotyping by sequencing for biogeography Journal of Biogeography 50 2 262 281 doi 10 1111 jbi 14516 Heffelfinger Christopher Fragoso Christopher A Moreno Maria A Overton John D Mottinger John P Zhao Hongyu Tohme Joe Dellaporta Stephen L 2014 Flexible and scalable genotyping by sequencing strategies for population studies BMC Genomics 15 1 979 doi 10 1186 1471 2164 15 979 PMC 4253001 PMID 25406744 Tassel 5 GBS v2 Pipeline Tassel 5 Source Retrieved 20 May 2016 Retrieved from https en wikipedia org w index php title Genotyping by sequencing amp oldid 1188182513, wikipedia, wiki, book, books, library,

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