plant genotyping in cotton

The discovery of novel single-nucleotide polymorphisms (SNPs) is critical for plant genotyping to provide many candidate markers for marker-assisted selection programs in key crops. Recent improvements in real-time PCR and next-generation sequencing have simplified SNP discovery and made it much more cost effective. Life Technologies offers a range of solutions to streamline all of your resequencing investigations and empower you to achieve your experimental and production goals.

Read the interview with Franziska Turck at MPI Cologne (Germany) discussing the advantages of mapping by sequencing in her Arabidopsis work.

Why are SNPs Important?

SNPs are small variations in the DNA sequences that are associated with desired traits. They are used in conjunction with quantitative trait loci (QTL) mapping to develop assays for marker-assisted selection programs aimed at improving or enhancing certain characteristics such as higher yield, better stress tolerance, or enhanced pest resistance.

Plant targeted resequencing and SNP analysis solutions by Life Technologies

Discover new SNPs in important crop variants using a targeted resequencing strategy on the Ion Personal Genome Machine™ (PGM™) . Then confirm your discoveries either with TaqMan® Assays, the gold-standard for targeted SNP analysis ,or by Sanger sequencing on one of the Applied Biosystems® 3500 Series Genetic Analyzers.

The table below compares the best solutions across our portfolio:

Research Need Best experimental approach Life Technologies platforms Why
Compare sequences of several variants of my crop to discover functional SNPs Genotyping by sequencing (GBS) Ion Torrent PGM™
  • Speed, cost, scalability, simplicity
  • PGM™ also allows you to take on genotyping by sequencing (GBS) applications
Map up to 10 SNPs in different regions of the genome Fragment analysis

SNP genotyping using CE

3500 Series Genetic Analyzers

  • Multiplexing capability: up to 10 SNPs per reaction
Map SNPs in a small region of the genome Sanger sequencing

Sanger sequencing using CE

3500 Series Genetic Analyzers

  • Gold standard for sequencing
  • Accuracy, low cost
  • Simple workflow
Confirm my putative SNP and develop SNP assays for downstream work Genotyping by Real-time PCR in Plants

TaqMan® SNP Genotyping Assays

TaqMan® Master Mixes

Real-time PCR instruments

  • Easy and fast workflow
  • Gold standard for targeted SNP analysis
  • High call rate and accuracy
  • Different formats for different project sizes
    (# of SNPs x # of samples)

Copy Number Variation Analysis Using TaqMan® Assays

TaqMan® Copy Number Assays can be used to obtain specific, reproducible, and easy-to-interpret copy number results in plant samples. In addition, this method is fast and simple, and the workflow can be automated so that several hundred to thousands of samples can be processed in a single day. Order assays here.