I am looking for a fast protocol to test purity of large seed samples preferentially using SSR markers on agarose gel. But if there is any other method for seed purity evaluation using PCR technology, kindly share it with me. By the way, I am working on rice.
test for purity in the sense of GMO free? This company offers various test kits, indended for diagnostics mainly, but the may be applicable for your needs:
http://www.r-biopharm.com/products/food-feed-analysis/gmo/qualitative/item/surefood-gmo-libertylink-rice
Thank you Regina. I will visit the link. I am not however working with GMO yet.
I am just looking for seed purity of released varieties ( developed through conventional breeding) that have been multiplied by third party, prior to delivery to farmers. What should be the size of a sample to be user? 20, 50, 100 grains? What is the minimum level of mixture that can be detected on agarose gel (2, 5, 10% or more). I am assuming I have at least 1 identity marker for my variety to be tested for purity.
Thank you
If it is your own variety then you need to identify a few unique SSR markers that are specific to the variety and use the same. You can use the SSRs from the parents used to produce the new variety and identify the specific ones
Based on work done with sorghum and SSR markers by a PhD student of mine nearly 10 years ago at ICRISAT-Patancheru, we could detect a the presence of a 2nd SSR allele with as little as 10% of the template DNA having the low-frequency allele. However, this assumes that the low-frequency allele is not a null allele, and that there is no overwhelming preference for template DNA of the more common allele in the PCR reaction. To start, I would collect bulk DNA from 20 sets of 5 seedlings each, and then use these20 bulks as template DNA for pre-PCR multiplex PCR runs with three SSR primer pairs that can detect alleles that are relatively uncommon in the crop germplasm as whole, but that are present in the particular genotype that you are attempting to assess the purity of. If banding patterns for these three markers look OK, then the seed lot is probably OK.
I go with Tom but I would like to add that though a unique allele or set of alleles is the best way to assess seed purity sometimes the allelic variation may not be reflected in the phenotypic characteristics one may be interested in for commercializaiton
Please mention the crop to be tested before release to the farmers.
in common genetic purity for open pollinated crops 98% and for Hybrids 95%.
Hope answer is suffice
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