https://www.researchgate.net/post/What_is_the_fastest_way_to_learn_how_to_perform_GWAS_Association_mapping_in_plants_using_GAPIT_an_R_package_What_are_the_available_resources2

What is the fastest way to learn how to perform GWAS (Association mapping) in plants, using GAPIT (an R package )? What are the available resources?

I’m trying to perform GWAS for the first time using R (GAPIT) and I would like to know how to start as a beginner and how to get to the actual analysis step ASAP. My genotyping data is SNP (90K) and my phenotypic data involves yield, agronomic traits, as well as canopy temperature depression of winter wheat association mapping panel of 300 genotypes in 4 different environments (2 locations x 2 water regimes).

回答一

Nick VL Serão

That’s a complicated task: teach you how to perform GWAS ASAP from my computer…
As you even mentioned, there are many different software for this. You chose to use GAPIT in R. You can use SAS, GenABEL (in R as well), qxkap, ASReml, PLINK, and more..
All of these methods are based on a single-SNP type of analysis, testing one SNP at a time, treating them as fixed effects. Some of these software allows for random effects (SAS/ASReml/qkpak) and some also allow the use of relationship matrices (ASReml and qxpak).
Other methods, as those implemented in GenSel, fit all (of several) SNPs simultaneously in the model, as random effects. These are known as Bayesian methods (BayesA, BayesB, BayesC, etc..), and are usually used for genomic prediction, but have been shown to be very good for GWAS as well.
I’ve found these slides online showing how to use the R package you chose: http://pbgworks.org/sites/pbgworks.org/files/GAPIT_with_SYslides.pdf
Performing GWAS is not complicated, but you need to pay attention to your model.. What are ALL possible sources of variation that you have? Do you have 300 different genotypes, or 300 individuals within genotype? What’s your sample size?
Some of these software also allows for interactions between SNPs and effects in the model (e.g. SNP x Location).
Nick

http://pbgworks.org/sites/pbgworks.org/files/GAPIT_with_SYslides.pdf