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Malawian groundnut variety identification using DNA fingerprinting
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Malawian groundnut variety identification using DNA fingerprinting

  1. Malawian Groundnut Variety Identification Using DNA Fingerprinting Sep/2010 Santie de Villiers,Vincent Njunge,Moses Siambi,Emmanuel Monyo ICRISAT-Nairobi and ICRISAT-Lilongwe For legumes, such as groundnuts, it is often difficult to differentiate the seeds from various varieties and to be sure that seeds are genetically“true-to-type”. Conventionally, seed samples are drawn from large lots and planted so that the morphological features can be compared against a set of descriptors,but this takes time and is expensive. The identification of molecular markers that can be used for variety identification through DNA fingerprinting is not only quicker but also cheaper.Any plant tissue (seed, leaf, root) can be used at any stage of growth and it is not dependent on the particular cropping season. Identification of fingerprinting markers • Nuclear seed from breeders and/or genebank accessions of all cultivated varieties (six released varieties and 13 local ones) were sent for analysis in Nairobi at the BecA-ILRI hub • The seeds were planted and DNA isolated from seedlings • The isolated DNA from all the varieties was analyzed by genotyping with 20 publicly available GCP SSR markers (http://gcpcr.grinfo.net/ index.php?app=datasets&inc=search_simple) and results visualized using an ABI3730 sequencer. • From the 20 markers used, three were identified that can distinguish all 19 varieties. They are: - TCF12 - TC7H11 - 5D5 • Training of Malawi seed system unit staff in sampling, DNA extraction and PCR technology that can be done in-house. DNA fingerprinting process • Seed inspectors or breeders collect samples from seed lots and/ or farmer fields according to an internationally approved sampling protocol • Samples are sent for DNA fingerprinting to an appropriate facility such as ICRISAT-India, BecA-Nairobi, the Malawi Seed Systems Unit or an outsourced company/laboratory) • DNA extraction and genotyping with the three fingerprinting markers • Comparison of test samples with DNA from each documented variety • Confirmation of sample identity and purity • Results sent back to SSU for certification Applications • Assist in seed certification through : confirmation of varietal identity seed purity testing/confirmation • Tracking of disseminated varieties in farmers’fields to adoption of released varieties and a measure of the impact from the release of new varieties. An example of a groundnut DNA fingerprint displayed on an agarose gel. The known fingerprints are on the left (no’s 1 to 6).The unknown samples on the right are compared with these known fingerprints – a matter of matching the bars. In this example, the column with the arrow is clearly the same as known variety no.3,which is the fingerprint for variety Baka/ ICGV-12991. With funding from Irish Aid in 2010, ICRISAT has identified a set of three DNA markers for groundnut that can distinguishallthelocalandimprovedgroundnutvarietiesthatarecultivatedinMalawi.Thisgeneticfingerprinting technique will assist both breeders and seed regulatory agencies in ensuring that seed quality standards are maintained in the Malawi Seed Alliance and through maintenance breeding.
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