Analysis of soybean non-nodulation mutants by DNA amplification fingerprinting and bulked segregant analysis

In this study, two techniques were combined in order to create a more efficient means to isolate molecular markers for two unlinked non-nodulation loci in soybean. These two techniques had not previously been used in unison but have been shown to have characteristics sufficient to meet the goal.

These techniques are: 1) DNA Amplification Fingerprinting (DAF) and 2) Bulked Segregant Analysis (BSA). DAF is a technique that employs the use of arbitrary primers to amplify many regions of genomic DNA. BSA is a technique of pooling individuals from a population into bulks based on a phenotypic trait that can be scored. In using these techniques together, BSA was supposed to isolate molecular markers in one bulk so that DAF could be used to detect that difference.

The results were not as expected and no linked markers were isolated. The focus then turned to analyzing the experimental design to find exactly why the anticipated results were not obtained. It was found that the nature of the genome contributed most of the problems. The fact that these loci are in regions of conservation and that the soybean genome is most likely duplicated are major contributions to the pitfalls of the project design. Competition during amplification of the DNA also seems to have some effects.

Suggestions to make the next effort in isolating markers more successful included the removal of the BSA technique from the project design.