Genotyping-by-sequencing (GBS)
Usually genome sequencing is used for identifying the SNPs but it is very costly offense for most genome especially complex genomes like plants. Plants possess most complex genomes due to ploidy variability and are difficult to sequence completely. The flexibility and low cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. GBS gives an advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping.
Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers.
Application of GBS to breeding, conservation, and global species and population surveys may allow
- Plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools
- Conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species
GBS uses Illumina next generation sequencing platform to discover thousands of SNP markers in numerous model or non model organisms. GBS givens an opportunity for studying SNPs and markers in all it is a "complexity reduction" technique designed to reliably interrogate a segment of genome; the method involves cutting down a genome anywhere from 0.1 to 15% with at least one restriction enzyme and sequencing the ends of the resulting fragments for either genetic marker discovery or genotyping.
- Allows you to interrogate a scalable number of loci even in a highly heterozygous species that leads to study of QTL mapping and population genomics
- Enables "deep sequencing" of RAD‐tags at 30‐60 x coverage to discover SNPs, giving researchers confidence that technology can identify genetic variation linked to a trait or population
- The complexity of the genome is reduced by digesting the DNA with optimized enzymes
- The most commonly used enzymes in plants are PstI, SbfI, SgrAI, ApeKI etc, and in animals are SbI, PstI, NotI, Eag1, BamHI, BbvC1 etc. Combination of enzymes set can be used to prepare libraries for parental as well as progeny lines and sequencing on illumina platform using paired‐end library can be carried out by multiplexing for 96, 192 or more samples or as per request
