Capture-Seq

Capture-Seq is a targeted next generation sequencing (NGS) platform for characterising hundreds of thousands of targets (including complex polyploids). Samples may be comprised of a single species, a mix of closely related species or distantly related taxa. Capture-Seq is suitable for both high and low volume applications.

Finding needles in the genomic haystack

Capture-Seq is the most comprehensive targeted genotyping system for discovering and characterising the genome for:

Allele mining: Pre-breeding marker discovery
SNP genotyping and haplotyping
QTL mapping and candidate gene identification
Genetic fingerprinting
Polyploid genomic selection
Resistance gene sequencing (RenSeq)
Pan-genome construction and mapping
Any organism can be analysed using Capture-Seq, and we offer a suite of validated, ready-made Capture-Seq panels for industry-wide standardisation of genotyping data.

Resources

Targeted exome sequencing

Hundreds of thousands of targets
Predesigned and custom panels available
Legacy data compatible
Short and long read options
Illumina®
PacBio®

Tissue/DNA to Fastq data, SNPs and more

Minimum 500 samples for DNA extraction
Up to 5-week turnaround times

Repeatable and reliable

Sequence the same regions every time
<1% missing target data

Suitable for commercial and research agriculture

Low minimum sample number
Minimal ascertainment bias

Capture-Seq vs arrays

Genotyping system	Targeted genotyping data	Data interval per target	Development cost	Ease of customisation and adaptation	Missing data %	Ascertainment bias	Read depth at targets (equivalent sequencing)	Repeatability	Suitable for novel marker discovery	Suitable for haplotype reconstruction	Ease if copy number and dosage detection	Analytical complexity
Capture-Seq	Yes	400-500 bp	Low	High	Low	Low	Predictable and controllable	High	Yes	Yes	High	Low
Chip-based arrays	Yes	1 bp	High	Low	Low	High	N/A	High	No	No	Low	Low

Capture-seq technology

Answering multiple questions in tandem

Capture-Seq flexibly targets SNPs, genes, and QTLs at the same time to produce sequence data at each region, instead of a single SNP, through the power of NGS. This enables Capture-Seq to provide greater genomic insights into breeding material and training populations, including the ability to phase alleles into haplotypes for more effective polyploid results.

Easy and adaptive

Capture-Seq panels are suitable for different breeding programs of the same or closely related species, ensuring comprehensive pre-breeding marker discovery with minimal risk of ascertainment bias and wasted resources.

Capture-seq technology diagram (at the right)

Capture-Seq uses targeted probe hybridisation technology to selectively recover regions of interest throughout the genome of any species.

Capture-Seq probe targets are selected from reference sequence data including genomes and/or transcriptomes. After target selection, Biosearch Technologies designs and synthesises complementary probe sequences to enrich for target regions during sample processing.
Genomic DNA is processed to sequencing-compatible DNA libraries.
After DNA library preparation, Capture-Seq probes are hybridised to each sample to selectively enrich target regions over other non-targeted DNA sequences. This improves the proportion of sequencing data going towards regions of interest vs the overall genome.
After next generation sequencing (NGS), sample data from the target regions is analysed and markers are identified across all samples.
Markers can be further analysed for use in genomic selection, genome-wide association studies, insertion site characterisations and more.

Click to view diagram

Capture-seq genotyping results

Species	Genotyping objective	# Capture-Seq targets	# SNPs detected	Missing data %
Maize	Fine mapping resistance genes (R-genes)	5,000	4,623	0.15
Sugarcane	Genomic selection and genetic mapping	10,000	37,976	0.1
Loblolly pine	Genomic selection	20,000	67,525	0.002
Blueberry	Genomic selection and genetic mapping	31,000	205,057	0.03