Due to the development of new sequencing methodologies (or NGS for New Generation Sequencing) and the increase of whole genome sequences, it is becoming more and more tempting to study the genetic diversity at whole genome scale and revealing allelic variability directly by DNA sequence comparison.
Pangenomic studies, especially for species with large genomes, may however require reduction of genome complexity in order to become useful and economically acceptable.
Various strategies for reducing genomic complexity in order to study only a targeted part of the genome can be implemented depending on the species (and the complexity of its genome) and the research question. One of them consists of sequencing only the transcriptomic part, i.e. expressed genes, based on mRNA purification and sequencing of cDNA. Such a strategy was chosen in the Comparative population genomics sub-project (SP1). NGS application to whole transcriptome sequencing is also called RNA-seq and different protocols have been developed for allelic diversity analysis.
Other strategies are applied on genomic DNA, but aim to concentrate sequencing effort on the non repeated part of the nuclear genome, by partial elimination of cytoplasmic DNA and highly repeated nuclear sequences. One of the methods used for that purpose is based on DNA restriction using methylation sensitive restriction enzymes.
Application to genotyping implies to set up fast, low cost and robust procedures, allowing reliable analysis of large sets of accessions.
Although, all these strategies and methods produce de facto genotype information by DNA sequencing, the term “Genotyping By Sequencing” and its acronym “GBS” are currently used, by the scientific community, in the restricted case of complexity reduction using restriction enzymes (Elshire et al. 2011).
Next Generation Genotyping (NGG) has been proposed as the generic term including all the genotyping approaches using NGS (M.C. Le Paslier pers.comm.).
Since many species analyzed within ARCAD project are orphan or neglected plant species, most of the time they lack the genomic information available on more studied plants, which may make the use of GBS more difficult.