QTL Mapping and Marker-Assisted Selection
 Effective, high-throughput methods for marker-assisted selection, genotyping, copy number analysis, or detecting single-nucleotide polymorphisms (SNPs) are enhancing our understanding of how to breed crops with desired traits such as higher yields or better disease resistance. Life Technologies offers a wide range of technologies to facilitate your breeding and functional genomic studies, associate important traits with genetic variants (including SNPs and AFLPs), construct quantitative trait locus (QTL) maps, and identify genetic markers for marker-assisted selection (MAS) programs. |
What are QTL mapping and marker-assisted selection (MAS)?
QTL (Quantitative Trait Locus) analysis links genetic markers with DNA base variations, such as single-nucleotide polymorphisms (SNPs) and microsatellite or simple sequence repeats (SSRs) to the QTLs of interest for breeding purposes. These are then used in linkage mapping and downstream marker-assisted breeding programs to screen for individual plants that have the trait(s) of interest. Depending on the program, these traits could be increased yield, disease or stress resistance, or enhanced nutritional or oil profiles.
What is the best approach if I am using SNP markers for breeding?
Choosing the best experimental approach and technology platform depends on your specific needs. Two key elements to consider are the number of samples and the number of markers in your project. The chart below gives a high-level representation of the different technologies we have to assist you in selecting the right plant seed line, moving a transgenic plant to the greenhouse or the field, or collecting critical data for your publication.
Genotyping by sequencing (GBS) the
IPGM™ System
- Low cost for total project
- Fast and easy workflow
- Flexibility
- Affordability
TaqMan® Assays or HRM
- Easy workflow
- Fast
- Gold standard (TaqMan®)
- High call rate and accuracy (TaqMan®)
- Very low cost (HRM)
Fragment analysis on a genetic analyzer
- Up to 384 samples, 10 microsatellites
- Multiplexing capacity
TaqMan® Assays QuantStudio™ OpenArray® System
- Low cost
- Proven TaqMan® chemistry
- Streamlined workflow
- Reduced consumables
and steps
TaqMan® Assays on Douglas Array Tape™
- High throughput
- Automated workflow
- Low cost
- Proven TaqMan® chemistry
How do the different approaches compare to each other?
| Fragment analysis (SRRs) | Genotyping by sequencing IPGM™ System | TaqMan® Assays regular qPCR instrument | High- resolution Melting Analysis (HRM) |
TaqMan® Assays QuantStudio™ OpenArray® | TaqMan® Assays on Douglas Array Tape™ | |
|---|---|---|---|---|---|---|
| Sample throughput | 1–500 | 1–1,000 | 1–500 | 1–500 | 500–4,000 | 500–millions |
| Marker throughput | 1–100 | 100–5,000 | 1–100 | 1–? | 16–512 | 1–100 |
| Cost per data point | Medium | Low-to-Medium | Medium | Very low | Low | Very low |
| Formats and flexibility | Multiplex up to 20 SSRs per sample | IAmpliSeq™ Custom Panels (primer pools) can be used to analyze up to 1,536 amplicons in 16 samples a single 318™ chip | Single tube, 48-well, 96/96 FAST-well, and 384-well formats | Single tube, 48-well, 96/96 FAST-well, and 384-well formats | OpenArray® plates plus four additional blocks for different sample/marker throughput | Array Tape™ Platform |
| DNA to answer | 4 hrs | 1 day | 40 min (FAST) 2 hr (Standard) |
1 hr | 4 hr | 3 hr to 1 day |
| Order instrument | Learn more > | Order now | Request a quote | Request a quote | Learn more > | Learn more > |
| Order consumables | Learn more > | Order now | Order now | Order now | Order now |
New to QTL mapping and market-assisted selection?
- Learn more about fragment analysis using Applied Biosystems® Genetic Analyzers
- Learn how the TaqMan® probe-based chemistry works
- Find out about SNP Genotyping Analysis using TaqMan® Assays
- Visit the HRM application resource page to learn about high-resolution melting (HRM) analysis and how it can be used
Scientific Resources | Technical Notes & ProtocolsSupport
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