NanoGBS: A Miniaturized Procedure for GBS Library Preparation

Frontiers in Genetics
Davoud TorkamanehFrancois Belzile

Abstract

High-throughput reduced-representation sequencing (RRS)-based genotyping methods, such as genotyping-by-sequencing (GBS), have provided attractive genotyping solutions in numerous species. Here, we present NanoGBS, a miniaturized and eco-friendly method for GBS library construction. Using acoustic droplet ejection (ADE) technology, NanoGBS libraries were constructed in tenfold smaller volumes compared to standard methods (StdGBS) and leading to a reduced use of plastics of up to 90%. A high-quality DNA library and SNP catalogue were obtained with extensive overlap (96%) in SNP loci and 100% agreement in genotype calls compared to the StdGBS dataset with a high level of accuracy (98.5%). A highly multiplexed pool of GBS libraries (768-plex) was sequenced on a single Ion Proton PI chip and yielded enough SNPs (~4K SNPs; 1.5 SNP per cM, on average) for many high-volume applications. Combining NanoGBS library preparation and increased multiplexing can dramatically reduce (72%) genotyping cost per sample. We believe that this approach will greatly facilitate the adoption of marker applications where extremely high throughputs are required and cost is still currently limiting.

References

Aug 2, 2003·Human Heredity·Rust Turakulov, Simon Easteal
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Mar 21, 2009·Genetics·D HabierJ C M Dekkers
Jan 16, 2010·Nature·Jeremy SchmutzScott A Jackson
Feb 16, 2011·Bioinformatics·Heng Li
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
May 23, 2012·Nature Methods·Shi WangMikhail V Matz
May 29, 2013·Molecular Ecology·Shawn R NarumPaul A Hohenlohe
Jul 23, 2013·PloS One·Qiang ChenYuchun Pan
Mar 4, 2014·PloS One·Jeffrey C GlaubitzEdward S Buckler
Sep 5, 2014·PloS One·Jeffrey M DaCosta, Michael D Sorenson
Apr 19, 2015·Genetics, Selection, Evolution : GSE·Gregor GorjancJohn M Hickey
Dec 25, 2015·Nature·Mauricio A UrbinaErin E Reardon
Dec 31, 2015·Genetics·Omar A AliMichael R Miller
Jan 6, 2016·Nature Reviews. Genetics·Kimberly R AndrewsPaul A Hohenlohe
May 18, 2016·Marine Genomics·Rute R da FonsecaRicardo J Pereira
May 26, 2016·Scientific Reports·Fábio PértilleLuiz Lehmann Coutinho
Sep 5, 2017·Plant Biotechnology Journal·Davoud TorkamanehFrançois Belzile
Oct 27, 2017·Genetics, Selection, Evolution : GSE·Jérôme RaoulJean-Michel Elsen
Jan 21, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Davoud TorkamanehFrançois Belzile
Feb 11, 2018·Genomics·Artur GurgulMonika Bugno-Poniewierska
Jun 3, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Amina AbedFrançois Belzile
Nov 22, 2018·Methods in Molecular Biology·Amina AbedFrançois J Belzile
Jun 8, 2019·Bioinformatics·Davoud TorkamanehFrançois Belzile

❮ Previous
Next ❯

Citations

Jan 22, 2021·Plant Biotechnology Journal·Davoud TorkamanehFrançois Belzile

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
chip
PCR

Software Mentioned

VCFtools
DepthFinder
TASSEL
GBS
NanoGBS
Fast

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.