Capture-Seq is the most comprehensive targeted genotyping system for discovering and characterizing the genome for:
Any organism can be analyzed using Capture-Seq, and we offer a suite of validated, ready-made Capture-Seq panels for industry-wide standardization of genotyping data.
Genotyping System | Targeted Genotyping Data | Data Interval per Target | Development Cost | Ease of Customization & 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 & Dosage Detection | Analytical Complexity |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Capture-Seq | Yes | 400-500bp | Low | High | Low | Low | Predictable & Controllable | High | Yes | Yes | High | Low |
Chip-Based Arrays | Yes | 1bp | High | Low | Low | High | N/A | High | No | No | Low | Low |
RADSeq/GBS | No | 90bp | Low | Very Low | High | N/A | Often Low | Low | Yes | Yes | Low | High |
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.
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.
Restriction enzyme genotyping-by-sequencing (GBS), sometimes called RADseq, datasets are inconsistent and produce high levels of missing data, especially in polyploid plants, making agricultural applications more challenging or impossible.
Capture-Seq leads the genotyping industry in low missing data. This ensures consistent, effective applications of breeding data to improve genetic gains.
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 |
Discover Flex-Seq® Ex-L for high-volume genotyping Learn about implementing genomics in breeding