New Methods and Resources (I)

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Published on: February 5, 2013

On this blog, I highlight a new method or resource pretty regularly. I used to work in what I think is a fairly normal UK plant science lab, so I try to comment on aspects I would have found useful to know about, for example if the method requires a machine not every lab has, or if it is unclear about anything. However, there are many, probably excellent, new open software and techniques which I don’t highlight on the blog because I am completely unfamiliar with their background.

For today, here’s the first part of a round-up of plant methods and resources published over the last few months. If you have used them, feel free to let me know how they worked in the comments, or through email or Twitter. And if you would like to review a method or resource for this blog, please get in touch!

iRootHair is a free, online, curated, expandable database of root hair genomics. Kwasniewski et al. (2013; Plant Phys. 161:28-35) built the database, which currently includes information about 153 root-hair related genes. The majority of the genes are from Arabidopsis, but maize, rice, tomato, and barley genes are also included. There is a page showing figures of various root phenotypes, which users can click through to see the genes associated with a specific phenotype; and a similar one for root processes like tip growth.

GWAPP, an interactive web-based application for conducting genome-wide association studies (GWAS) in Arabidopsis thaliana, was presented in December by Seren et al. (2012; Plant Cell 24:4793-4805). The guide on the resource website itself is very simple, so I suggest reading the paper in full before attempting to use it. There are currently 1386 accessions in the database, and users can map traits measured for just a subset of these accessions with a mixed model and mother methods. The application enables the user to view, select subsets, and choose an appropriate transformation before carrying out the GWAS, and presents the results in a quick summary and a number of graphical displays of data including population genetic statistics and linkage disequilibrium patterns.

For the sorghum researchers out there, this method from Covshoff et al. (2013; J. Exp. Bot. 64:807-13) adapts the leaf rolling technique of separating mesophyll and bundle sheath cells, which is usually used on maize, for use with sorghum. Although you will need to buy a mirVana miRNA Isolation kit from Ambion,  the only special equipment needed is a low-tech wallpaper roller from Homebase!

Image credit: Laboratory by Mandie LeScum via stock.xchg



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