SLAF-seq (Specific-Locus Amplified Fragment Sequencing) is a high-throughput genotyping method based on next-generation sequencing (NGS) and belongs to the group of Reduced Representation Genome Sequencing (RRGS). It was developed as a cost-effective alternative to whole-genome sequencing (WGS) for projects that require the identification of large numbers of genetic markers while maintaining high throughput and controlling costs.
SLAF-seq selectively captures defined genomic fragments by digesting DNA with appropriately selected restriction enzymes. The resulting fragments form a Reduced Representation Library (RRL), a representative library of selected genomic regions that is subsequently subjected to high-throughput sequencing.
Unlike conventional marker-based methods such as SSR or AFLP, SLAF-seq enables the simultaneous discovery and genotyping of hundreds of thousands of SNP markers in a single experiment. The technology can be applied to organisms with a reference genome as well as to species for which no reference sequence is available.
SLAF-seq workflow
- DNA integrity,
- sample concentration,
- genetic material purity,
- presence of potential inhibitors of enzymatic reactions.
- appropriate restriction enzymes,
- expected number of markers,
- fragment size range,
- sequencing depth.
- potential issues related to the genome of the target organism.
- the performance of the selected enzymes,
- the number of fragments generated,
- the library size distribution,
- potential issues related to the genome of the target organism.
Genomic DNA is digested with the selected restriction enzymes. The resulting fragments are then:
- size-selected,
- ligated to sequencing adapters,
- PCR-amplified,
- indexed (barcoded),
- prepared for sequencing.
Each selected fragment represents a potential genetic marker known as a SLAF tag.
Applications of SLAF-seq
SLAF-seq has broad applications in genetics, genomics and population biology.
- gene mapping,
- identification of QTL regions,
- studies of trait inheritance.
- gene mapping,
- identification of QTL regions,
- studies of trait inheritance.
- assessing genetic diversity,
- analysing population structure,
- studying gene flow,
- identifying evolutionary events.
- Marker-assisted selection (MAS). In breeding programmes, this technology supports:
- identification of favourable alleles,
- accelerated selection,
- improved breeding efficiency.
- Phylogenetic studies. The large number of genomic markers enables reconstruction of evolutionary relationships among species and populations.
Technical specifications of SLAF-seq
- Sequencing platform: Illumina
- Pilot experiment - included in every project (3 pilot samples, each tested with 3 different pairs of restriction enzymes)
- Amount of data per sample (output):
- 100k tags per sample - standard, recommended approach for organisms with genomes < 500 Mb
- 200k tags per sample (target organism genome size: 1 Gb-2 Gb);
- 300k tags per sample (for large and complex genomes);
- 400k tags per sample (for large and complex genomes);
- Other / Custom (available upon special request).
- Recommended Sample Requirements - DNA/RNA:
- Sample type: gDNA
- Amount: > 80 ng
- Concentration (NanoDrop): >10 ng/μL
- Volume: >20 μL (minimum 15 μL)
- Purity (OD260/280): 1.6 - 2.5
- GWAS analysis is available for projects involving more than 200 individuals
SLAF-seq bioinformatics analysis
After sequencing, the data undergo a multi-step bioinformatics analysis, included in the package price, comprising:
- Data quality control
- Mapping to the reference genome
- SLAF tag identification
- SNP discovery
- SNP annotation
- Insertion and deletion (InDel) identification
Selected projects and client publications
See which institutions we perform next-generation sequencing (NGS) for and explore scientific publications that draw on the data we have supplied.