spiked GBS and looking for adaptive genes
spiked GBS pipeline, from Rife et al. (2015).
Hello everyone! To our donors - thank you for your support! If you have not yet received a thank you message, it is on its way. We are working on interesting things for backer incentives - but at minimum, we will share progress with you as backer-only lab notes once the project is up and running.
For the time being, we wanted to let you all know about an under-used method for finding molecular markers both throughout the genome and in targeted regions. While traditional Genotype-by-Sequencing (GBS) is great for finding lots of markers, it is very difficult to trace those markers back to genes of known function without a reference genome for the species of interest. This is not the end of the world, because you can still look at how variation in markers related to climate variables is distributed spatially, as this could provide some solid evidence of how climate conditions have shaped adaptation; however, you still cannot say anything about what traits or functions climate may be influencing in this way. Since we do not have reference genomes for these two species, we are interested in other ways of both a) getting lots of markers, and b) still saying something about how climate may shape variation in genes of known function.
Spiked GBS (sGBS for short) combines the non-targeted approach of standard GBS with more targeted, candidate gene-based approaches. By using this approach, researchers can search a species' genome for molecular markers, while also identifying markers in genes of known function. We hope to use this novel approach, developed in 2015 by Trevor Rife and colleagues, for our own study. Although this approach has only been used for agricultural crop genomic research so far, we think it will work great for our study system.
Thanks for reading - next time, we will talk about possible gene targets, analytical methods, and/or conservation applications for this work! And as always, you can help us share this project by using the following link: https://experiment.com/turtle-climate-change-genes
-Nathan and Brendan
P.S.: For those interested, here is a citation for and link to the spiked GBS paper:
Rife TW, Wu S, Bowden RL, Poland JA. Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling. BMC Genomics. 2015;16(1):248. doi:10.1186/s12864-015-1404-9.
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