Question

Explanation Of Results Of Gwas For Control And Stressed Condition

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11.4 years ago

kumar.vinod81 ▴ 330

Hi, I have some confusion regrading results of GWAS conducted for a diploid plant species for Na content measured under control and under salt imposed condition. I've measured Na content from plant under control (without salt) and salt imposed condition. I got 32 highly significant (FDR corrected) SNPs only under control condition while I am not getting any of the significant SNP under salt imposed condition. Is it mean that my study is not fruitful or still I can say something about. Can you researchers here, help me in this regard. Thanks

Vinod

gwas • 2.2k views

ADD COMMENT • link updated 11.4 years ago by Michael 54k • written 11.4 years ago by kumar.vinod81 ▴ 330

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I hope you have more than 2 plants.

ADD REPLY • link 11.4 years ago by Neilfws 49k

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No, Single plant genotype was evaluated under control and stressed condition, and 220 genotypes were used for this purpose.....

ADD REPLY • link 11.4 years ago by kumar.vinod81 ▴ 330

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You really need to specify more details of the experiment and your analysis because right now, it sounds like GWAS with one individual. And that makes no sense at all, since GWAS is all about variants.

ADD REPLY • link 11.4 years ago by Neilfws 49k

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we have selected 220 different plant genotypes and each genotype was genetically pure. We have selected only those genotypes which were differ in salt tolerant ability and evaluated them in different trial specially designed for salt tolerance and compared them with control plants (without salt tolerance). 20 plants were observed for this purpose and averaged them and used in GWAS experiment. Actually Na content in plant was observed for this salt tolerant ability of plants in control as well as in salt exposed condition. Tolerant plants always maintain minimum level of Na in their system and produce well while susceptible plants will have maximum level of Na and will show the signs of salt intolerance. 6000 genome wide SNPs were selected for this purpose. I've used TASSEL for this purpose and find out that only Na content in control condition is associating with a number of SNPs, but no SNPs is associating with Na content in salt exposed condition. I've not SNP imputation as I dont know much about it. Please share your ideas so i can go ahead...... Thanks

ADD REPLY • link 11.4 years ago by kumar.vinod81 ▴ 330

score 3 · Answer 1 · 2012-11-23

Unfortunately, it looks like the experiment is flawed. From your description it appears that what you did was (you should really describe your methods better, another indication for that something went wrong): Took 220 monoclonal plants (genetically identical individuals) derived from e.g. a single parent plant, divided into two groups, planted them out and exposed the two groups A,B to two different conditions (e.g. salinity) for some time, and let them grow then harvested the same plants and did a GWAS (you sure you did a GWAS at all?). At least that is what you wrote above, if your setting was different, then you need to describe it better.

Unfortunately, if this is true, you have completely wasted your efforts. How is genomic variation going to enter this picture? It doesn't. You needed to grow your plants over a large number of generations of exposure to stress or selective pressure to see accumulation of variation Because of that the plants will still be genetically identical. Therefore, the outcome (no significant variation) is expected.

Your experimental setup would make sense for a gene-expression type of study though, gene regulation should respond to Na stress. That is why I am asking you whether you are sure you really did GWAS.