Question: Strategy help: searching for potential gene degradation (domestication)
gravatar for peter_stokes
16 months ago by
peter_stokes10 wrote:

Hi biostar community!

I am hoping for some advice on where to start for a project I have in mind.

Say, I am studying the domestication of species X. I have various elite cultivars, landraces, and wild accessions of species X. An elite cultivar of species X has been studied in moderate depth and improved for agricultural applications (also has sequenced, assembled, and annotated genome). This plant is quite successful (compared to wild lines) for the traits selected for in its domestication/improvement. Due to the method of domestication, I suspect traits involved in sustainable agriculture have been degraded.

The problem is, these traits have not been annotated or really studied because these traits are found to be unimportant for yield, pathogen resistance, drought tolerance, etc. because of the conditions the plant will be grown in (agricultural settings with plenty of money for fertilizers).

My question is, how would I go about comparing the wild accessions of species X to the domesticated elite cultivars of species X? How would I go about performing a GWAS experiment to test whether or not the traits I suspect to be degraded are really degraded or not? Is this possible if these traits have not been annotated or studied in this system? I am not even sure where to start! All help is greatly appreciated!

snp alignment assembly genome • 330 views
ADD COMMENTlink written 16 months ago by peter_stokes10

Your question is vague, so, here's a vague comment: why not perform RNA-seq on your samples and then de novo assemble and [attempt to] annotate the assembled transcriptomes with Trinity? If you identify statistically significantly different transcripts that remain entirely unidentified, you can run them through blastx in order to infer functionality by comparison with known sequences in other species.

ADD REPLYlink written 16 months ago by Kevin Blighe46k
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