Thus far we have used SNPs makers to make a genetic/molecular linkage map and to find linkage between marker and whitefly resistance. Since there are a tremendous amount of SNPs in the genome and the fact that these markers can be analyzed in bulk (by using sequencing technology) makes SNP analyses a perfect tool for this. However, once linkage is found between a SNP marker and the resistance trait, using this kind of SNP analysis for selection in Marker Assisted Selection (MAS) is not a good choice. Sequencing all the DNA of all plants in a breeding population is very expensive and not very efficient if you are only interested in 1 marker/locus. Therefore, we use another type of marker to follow the resistance trait and perform MAS in a breeding program, namely KASP. This technology is very cheap (8-12 eurocents per data point) and very reliable. For small scale breeders it is also a very handy technology because this work can be outsourced.

KASP stands for Kompetitive Allele Specific Polymorphism.

Go to YouTube and watch the movie:

LGC's KASP Genotyping Chemistry Explained: KASP analysis & benefits of KASP

https://www.youtube.com/watch?v=GJbM7UbE7ZI

 

Next go the LGC Group website: https://www.lgcgroup.com/

Go to the Products and click on  Genotyping software.

Click on SNPviewer and download SNPviewer

SNPviewer is a tool that enables genotyping data to be viewed as a cluster plot (Figure below). Opening genotyping service project results in SNPviewer will allow you to view the genotyping clusters plate by plate. Genotyping calls cannot be changed within SNPviewer.

SNPViewer

Install SNP viewer. You will need administration rights on your PC to install SNPviewer ( In directory software)


After installing the SNPviewer (lgcgenomics_snpviewer_installer in directory software) you can load data with the data set called genotyping-019.001-01. In total 7 SNP markers have been scored.


Questions KASP

7.1   Why are some spots red and some blue and some green?

7.2    Is the SNP flanking the primer of is it part of the primer?

7.3   Why do you think the outsourcing factory wants the SNP and the sequence of 75 bases on both sides of the SNP?

7.4   What is important for the mutual primer in the KASP reaction

7.5   In the lower part a microtiter plate is shown, can you relate it to the picture above it

7.6   Can you combine 1 SNP for all plates in one picture (use view in heading)

7.7   If you open another dataset (Genotyping-035.016-01) you see no red spots, only two clouds are seen. Can you explain that?

7.8   With which plants do you go on in your breeding program, homozygous (both alleles giving resistance) or heterozygous (one allele giving resistance and one allele not)? Remember: Tomato is sold as an F1 hybrid meaning that the seeds are the result of a cross between a maternal and paternal plant.

7.9   You have two linked markers to an important gene, is it important whether they are both flanking the gene on the same side or do you prefer that they are on both sides. And why?