Analysis of Milkweed Genotyping

With just a few individuals left to send off as redos, most of the focus on the milkweed project has moved towards analysis. Analysis is inherently tricky because there is a lot of trial and error. There are essentially a few options for analysis. You can use someone else’s software, you can modify someone else’s to fit your needs, OR you can make your own. The last one is obviously extremely time intensive, so our hope was to find a software we could use to fit our needs.

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Going with the flow: a new and improved milkweed project, finally getting results

If there’s one thing that I’ve learned from my three years of research, it’s that its super important to go with the flow. Since my last update my milkweed project has taken on an entirely new shape. After discovering that glyphosate herbicides do not act as a proxy for connectedness, I decided to use a different approach and expand on my project from last summer.

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Milkweed Connectedness Update 1:

My original plan was to use common Milkweed as a study system to understand the impact of clonality and group survival. By intentionally adding a pathogen, such as an herbicide, the spread of the negative effects can be witnessed in a clonally connected plant. The goal of this experiment is to see how far the pathogens travel in a patch, how long it takes for other plants to die, and if there is any preferential sharing. For instance, sometimes younger plants are favored in sharing. Herbicide will be used as a proxy for connectedness and physiological integration. 

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Herbicide Transfer through Clonal Milkweed

In this study I propose to use common Milkweed as a study system to understand the impact of clonality and group survival. By intentionally adding a pathogen, such as an herbicide, the spread of the negative effects can be witnessed in a clonally connected plant. The goal of this experiment is to see how far the pathogens travel in a patch, how long it takes for other plants to die, and if there is any preferential sharing.

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Conclusion

The goal for this summer was to have sampling, DNA extraction, Polymerase Chain Reaction (PCR), and fragment analysis sent off (to be later analyzed) completed on all 400 of the subsamples. Sampling and DNA extraction were finished. PCR unfortunately was not, delaying fragment analysis as well. Though the PCR protocol was developed during spring semester of 2017, new primers and a host of other problems made this step tricky. The first batch sent off for analysis came back blank, requiring adjusting of the protocol and the second had nebulous results. A delay in shipment meant that only 3 of the 7 primers were available for much of the summer. However, all extractions were completed successfully, and in the last remaining weeks of July, PCR was done on all 400 of the plants for 3 of the primers. All PCR products were shipped off for fragment analysis. Training began on using a fragment analysis software, so once results do come back, analysis will be smoother.

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