Resources‎ > ‎


  • What are the advantages of SNPs over Simple Sequence Repeats (SSRs)?           




 Single Nucleotide Polymorphism (SNP)

  • Varying levels of multiplexing 
  • Provide robust automated allele calling
  • Produce high quality data which can be 
  •  easily merged across groups
  • stored in databases regardless of the genotyping platform used
  • Enable efficient, high-throughput processing of samples with increased speed and lower cost per data point
  • Provide a high density of markers  near a locus of interest
  • Evolutionarily stable, not changing significantly from generation to generation

  • Uses more DNA samples than SSR

Simple Sequence Repeat (SSR) 

  • Requires very small  quantity of DNA (5 ng/ reaction)
  • Can be run on commonly available lab equipment
  • Genetic codominance, abundance, dispersal throughout the genome, multi-allelic variation, high reproducibility and high level of polymorphism
  • very useful for population genetics, variety identification and protection, monitoring of seed purity and hybrid quality, gene tagging

  • Constraints in:multiplexing
  • Automation
  • Difficulties in sharing 

    data between labs due to differences in  relative allele sizes across genotyping platforms

  • High development costs associated with the identification of DNA sequences flanking SSRs
  • Only useful for closely related germplasm sources

Read More:Selectionof highly informative and user-friendly microsatellites (SSRs) for genotypingof cultivated potato M.Ghislain, D. M. Spooner,F. Rodriguez, F. Villamon, J. Nunez, C. Vasquez, R. Waugh, M. Bonierbale

  • What is the difference between the Illumina BeadXpress system from Fluidigm system?

Illumina Beadxpress functions as a miniaturized array platform with a high level of assay multiplexing and scalable automation. This system uses a high-density BeadArray technology in combination with an allele-specific extension, adapter ligation and amplification protocol or the GoldenGate genotyping assay.

Fluidigm EP1 system uses the innovative fluidic circuit (IFC) which can be compared to a semiconductor industry where there are networks of discrete pathways and intermediate switches. Instead of electrons, molecules of biological samples and reagents are moved in variety of patterns. This platform is suited for mid-multiplex genotyping at very high throughput using dynamic arrays. The matrix of channels, chambers and valves perform the complex work of assembling the arrays.

Read More:High-throughput SNP genotyping on universal bead arrays Richard Shen , Jian-Bing Fan, Derek Campbell, Weihua Chang, Jing Chen,Dennis Doucet, Jo Yeakley, Marina Bibikova, Eliza Wickham Garcia,Celeste McBride, Frank Steemers, Francisco Garcia, Bahram G. Kermani,Kevin Gunderson, Arnold Oliphant

Fluidigm EP1 System

  • Why do we need to provide the generation information of our samples in the forms?
Generation information is important in order for us to determine the Alchemy F-values or the inbreeding coefficient that will be used for the analysis of the data.

  • What are the parameters/criteria needed for SNP selection?
There are several parameters to consider for the selection of SNP which includes being bi-allelic and single copy, absence of SNPs within 60bp on either side of target SNP, none of the SNPs were in perfect LD with any other SNP within 500kb, high frequency of polymorphism within major subpopulations of O. sativa and good distribution throughout the genome.

Read More:
Development of SNP genotyping assays and applicationsin rice authentication  Chih-Wei Tung

  • What is the advantage of using Alchemy values right after running the data in the Genomestudio Software?
GenomeStudio software is based from human genome, thus, implicating difficulties in defining the heterozygous cluster. In comparison with ALCHEMY, the latter has been optimized to deal with highly inbred samples, therefore, providing more accurate allele calls. The genotype inference of ALCHEMY is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach. Furthermore, this incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels (Wright et al. 2010).

  • What are the information that can be derived from SNP?
Several information can be acquired from SNPs such as the genetic similarity between accessions, identification of F1 hybrid genotype, subpopulation assignment, tracing of the origin of introgression, discovering SNP contribution to agronomic traits and can also determine sample mix-up.

Read More: Development of SNP genotyping assays and applicationsin rice authentication  Chih-Wei Tung

  • What is the frequency of SNPs?
SNPs are found to be abundant in humans as well as in other plant genomes. The frequency of SNPs in humans is ∼1 per 500–1000 bp which is relatively lower than in plants.

Read More:PlantGenotyping II SNP Technology by R.J. Henry

  • If my plant DNA samples are not rice, can I still submit it for BeadXpress or Fluidigm?
As of now our Genotyping Service Laboratory only caters samples derived from rice. Processing of samples other than rice is not possible for the moment.

  • Can I customize my own markers?
Customization of markers for Fluidigm is possible. See Prices and contact us for further information.
Customization in BXP is not possible since the markers used for this platform is fixed. Only two kinds of OPAs are offered: indica x indica and indica x japonica.

*For more inquiries, contact us.