IAEA Teams with ILRI to Present Training Course on DNA Analysis of Small Ruminant Genetic Resources

The IAEA Coordinated Research Project (CRP D.3.10.25) "Gene-based Technologies in Livestock Breeding: Characterization of Small Ruminant Genetic Resources in Asia" was started in December 2004 with the overall objective of characterizing the small ruminant genetic resource of Asia. For this to be realized it was recognized that there is need to build capacity in the participating countries, thus enabling them to conduct research in livestock genetics using modern molecular methods. Therefore, the first phase of CRP provided an opportunity for scientists from six Asian countries to train in microsatellite genotyping at the International Livestock Research Institute (ILRI) and at the same time define the genetic characteristics of the small ruminants from their respective countries. Scientists [pdf] from 6 countries participated.

The CRP collaborators collected blood samples from sheep and goat breeds that are native to their home country. The blood was preserved in "magic buffer" and a questionnaire filled for every individual. Genomic DNA was extracted in the host lab and samples were shipped to ILRI. Samples [pdf] of DNA from 29 breeds of goats and 15 breeds of sheep were collected by the participants.

Prior to the hands on training the participants received a one day orientation on the following (1) course overview, procedures and expectations (2) health & safety issues including material safety data sheet and (3) instrumentation. The participants were also supplied with a manual that contained some basic principles of molecular genetics, the wet lab protocols to be followed and flow chart instructions of the commonly used population genetics software. The practical training started with buffer preparation and agarose gel electrophoresis and this allowed the participants to assess the quality of their DNA samples by electrophoresis.

The second phase of the training involved: setting up PCR reaction, thermocycling, evaluation of the success of PCR amplification and trouble shooting. This training allowed the participants to independently set PCR reactions and trouble shoot as required.

The next phase of training involved the following tasks (1) setting up of genotyping reaction (2) preparation of automated DNA sequencer sample sheet (3) co-loading of microsatellite markers (4) GENEMAPPER software analysis (5) electropherogram interpretation (6) peak editing (7) data export (8) quality control and (9) consolidated of genotyping data. On completion of all the tasks the participants were able to independently analyze DNA with minimal supervision. After two months of training and DNA analysis each participants was able to analyze 15 loci [pdf] in the goat samples. The participants were also trained in computational data analysis using a set of seven types of software [pdf]. The tasks in computational analysis included software installation, software running and data interpretation. Each participant was also provided with a CD containing the software to enable them refine their skills on return home.

The primary outputs of the training were:
- Training manual [pdf] in microsatellite genotyping
- Data base of animals sampled
- DNA samples repository
- Capacity building in molecular characterization of livestock
- Genotyping data ready for computational analysis