Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley
Open Access
- 3 October 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (10), e76925
- https://doi.org/10.1371/journal.pone.0076925
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.Keywords
This publication has 41 references indexed in Scilit:
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011
- VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in RBMC Bioinformatics, 2011
- Multiplexed shotgun genotyping for rapid and efficient genetic mappingGenome Research, 2011
- Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barleyBMC Genomics, 2011
- Genome-wide association studies of 14 agronomic traits in rice landracesNature Genetics, 2010
- Genomic selection in plant breeding: from theory to practiceBriefings in Functional Genomics, 2010
- Association Mapping: Critical Considerations Shift from Genotyping to Experimental DesignTHE PLANT CELL ONLINE, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Nuclear DNA content of some important plant speciesPlant Molecular Biology Reporter, 1991