Can anyone tell me which is the best method among the ddRAD or re-sequencing GBS for population Genotyping?
I have used GBS and it is very fast and efficient. There are pipeline developed for SNP scoring. See: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656875/
as well as others
Dear Vijay,
The attached papers
1-"Double Digest RADseq: An Inexpensive Method for
De Novo SNP Discovery and Genotyping in Model and
Non-Model Species " published in PLOS ONE May 2012 | Volume 7 | Issue 5 | e37135E covers the answer to your question.
The following is the abstract of the paper:
Abstract
The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via ‘‘SNP chip’’ microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotypephenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical
results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of
organisms.
Citation: Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and
Genotyping in Model and Non-Model Species. PLoS ONE 7(5): e37135. doi:10.1371/journal.pone.0037135
Editor: Ludovic Orlando, Natural History Museum of Denmark, University of Copenhagen, Denmark
Received February 1, 2012; Accepted April 13, 2012; Published May 31, 2012
* E-mail: [email protected]
2-So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute. Bull Mar Sci. 90(1):79–122. 2014
http://dx.doi.org/10.5343/bms.2013.1008
Abstract.—The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity
loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine
biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled “Genomic Applications to Marine Science and Resource Management in Southeast Asia” was
held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize
discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions.
Hoping this will be helpful,
Rafik
Hard to say, both have advantages and disadvantages. This review may help you.
http://www.nature.com/nrg/journal/v17/n2/full/nrg.2015.28.html
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