Hi everyone,
This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic diversity using DArT markers. Based on the charaterization result, i have selected 10 varieties to be subjected to water stress with the objective of identifying genes that are responsible for tolerance in this plant. My challenge now is:
1. bambara groundnut does not have a reference genome, so will i be able to use GWAS in getting these genes from the result of the DArTSeq.
2. Bearing in mind that the whole 95 varieties characterized were not subjected to water stress, do i need to set up another experiment entirely for the water stress and go ahead to make use of RNASeq to get the genes?
3. It is obvious that some genes will be upregulated and some will be downregulated, how do i identify these genes and how do i know if they are expressed at the onset of stress, during, or after stress?
4. when is the appropriate time to take my samples, i was considering taking at 50% flowering stage. Is this good?
Any help and insightful articles will be greatly appreciated.
Thank you.
Both would be useful and yield complementary information. Depending on whether there is a genome assembly for your species of interest, gwas would provide insight into candidate variants/regions underlying stress resistance. If you have access to live plants, RNAseq is definitely a viable option to detect differencial gene expression. Gwas would shed light on the blueprint while rnaseq would bring about insight on the molecular machinery involved in blueprint expression
Hi Oluwaseyi
They are both informative but consider these points: GWAS give you some important SNPs for you water stress experiment. These SNPs cannot tell you that how they act and in what tissue. If you choose to do RNA seq, sampling from one tissue might not cover all parts of story, therefore you may need to do RNA seq on different (or more important) tissues and this will add up to your experiment costs. By doing RNAseq you may obtain some info about SNPs by SNP calling if you have a suitable coverage.
Philippe Henry and Ali Javadmanesh , thanks for your responses. My major concern here is the lack of reference genome for this plant. Is there any other way i can go about it bearing in mind that there is no reference genome. I saw some articles talking about Isoseq method, don't know anything about this but do you think it can work for me here. Thanks
Hi Oluwaseyi
If this is a major project, I recommend to a whole genome sequencing with above 100X coverage and follow a de novo approach to establish your own ref seq. You may annotate it using annotations of closely related species. I would say this is another major project which will provide basics for any future NGS-based research on your species.
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