Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing

T, Ho; Cardle, Linda; Xu, Xin; Bayer, Micha; Prince, K. Silvas Jebakumar; Mutava, Raymond N.; Marshall, David; Syed, Naeem H.

doi:10.1007/s11032-014-0090-7

Cited by 7 publications

(4 citation statements)

References 33 publications

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“…To sequence genes or gene regions, targeted amplicon sequencing of individual or pooled samples using one of the NGS platforms is an attractive option (e.g. Homolka et al 2012;Ho et al 2014).…”

Section: Genomic Datamentioning

confidence: 99%

A practical guide to environmental association analysis in landscape genomics

et al. 2015

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Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reducedrepresentation sequencing, candidate-gene approaches, linearity of allele-environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.

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Section: Genomic Datamentioning

confidence: 99%

A practical guide to environmental association analysis in landscape genomics

et al. 2015

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“…For example, the Targeted Amplicon Sequencing (TAS) method uses a two-step PCR process to amplify specific targets across the genome and then add a barcode multiplex identifier across multiple individuals before pooling and sequencing (Bybee et al 2011). This method was further modified with a one-step PCR method for preparing amplicon tags for sequencing (Clarke et al 2014), and a related technique for Genome-Tagged Amplification (GTA) has been described for preparing sets of 96 samples x 192 amplicons (Ho et al 2014). There are also commercial kits available to enable amplicon sequencing, such as Illumina's TruSeq Custom Amplicon and the Ion AmpliSeq custom DNA panels; however, these have so far been limited to a small number of model species.…”

Section: High-throughput Snp Genotyping: Genotyping By Sequencing (Gbs)mentioning

confidence: 99%

High-Throughput SNP Genotyping to Accelerate Crop Improvement

Thomson

2014

Plant Breed. Biotech.

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Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP genotyping offers a number of advantages over previous marker systems, including an abundance of markers, rapid processing of large populations, a variety of genotyping systems to meet different needs, and straightforward allele calling and database storage due to the bi-allelic nature of SNP markers. NGS technologies have enabled rapid whole genome sequencing, providing extensive SNP discovery pools to select informative markers for different sets of germplasm. Highly multiplexed fixed array platforms have enabled powerful approaches such as genome-wide association studies. On the other hand, routine deployment of trait-specific SNP markers requires flexible, low-cost systems for genotyping smaller numbers of SNPs across large breeding populations, using platforms such as Fluidigm's Dynamic Arrays™, Douglas Scientific's Array Tape™, and LGC's automated systems for running KASP™ markers. At the same time, genotyping by sequencing (GBS) is rapidly becoming popular for low-cost high-density genome-wide scans through multiplexed sequencing. This review will discuss the range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities, and will provide an example of SNP deployment for rice research and breeding as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.

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“…The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long‐)amplicon sequencing (Rothfels et al, 2017) and hybridization capture (Mandel et al, 2014; Weitemier et al, 2014). Targeted amplicon sequencing is based on single‐fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR‐based amplification of multiple pre‐selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al, 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al, 2009) and was later applied to metazoan phylogenetics (Bybee et al, 2011; O’Neill et al, 2013).…”

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confidence: 99%