marker-assisted selection in corn

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 1–5001–1,0001–500 1–500 500–4,000 500–millions
Marker throughput 1–100100–5,0001–1001–? 16–5121–100
Cost per data pointMediumLow-to-MediumMediumVery lowLowVery low
Formats and flexibilityMultiplex up to 20 SSRs per sampleIAmpliSeq™ Custom Panels (primer pools) can be used to analyze up to 1,536 amplicons in 16 samples a single 318™ chipSingle tube, 48-well, 96/96 FAST-well, and 384-well formatsSingle tube, 48-well, 96/96 FAST-well, and 384-well formatsOpenArray® plates plus four additional blocks for different sample/marker throughputArray Tape™ Platform
DNA to answer4 hrs1 day40 min (FAST)
2 hr (Standard)
1 hr4 hr3 hr to 1 day
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