Hi Mohammad,

Actually you can use any publication related to genome-wide association despise the specie to guide you, specially the most cited ones. The Genome-wide association is a genetic tool that allows us to find the connection between phenotypic variation and DNA variation patterns. Usually we do it by creating a sample of individuals that we usually think that may represent the genetic pool of the specie.  We take these plants and crop them in the field and evaluate for some set of traits that we may be interesting to find some genes controlling them. Then, we take the same individuals and genotype them with some sequencing or microarray technology. We process the genotypic dataset for only informative variants (we remove loci without any genotypic variation), usually, trying to keep only those with allelic frequency of the reference allele above the threshold of 0.05 (what we call for filtering for MAF>0.05). After that, we take these genotypic data and try to seek if there is or not some structuration in the population, either using unsupervised techniques, like PCA, or supervised ones, like the one obtained by popular models like STRUCTURE etc. Then, we fit some linear regression process, either fitting markers individually, or using some set of them, and try to model for controlling population structure, either introducing indicator variables in the model for mapping the known structure obtained by PCA or STRUCTURE, or modeling the genetic effects of the individuals via linear mixed modeling, and mapping their relationship via kinship matrices, or both. Subsequently we test the molecular marker associations and make some multiple test correction or control for false positive via FDR. We get this associations and try to find if they were previous reported in some genomic database like UNIPROT (curated by humans) or NCBA. We then report the associations that matches with previous studies, and also report the new ones, and try to document everything in some genetic database (UNIPROT, NCBI, etc).

If I was helpful please recommend my answer, new people with the same doubt can have easily access to it too,

Best,

Association mapping is a method to identify /discover quantitative trait loci (QTLs) by taking advantage of linkage disequilibrium. To make it simple phenotypic data (traits etc.) are associated/compared to the genotypic data to know which QTLs / genes are responsible for the studied traits etc.

There are different models and softwares which can be used for association mapping depending upon your data and purpose, one of the most common one is TASSLE.

For Apple Scab you have go to go through literature.

Hope you got your answer 

Regards

There are several interesting reviews you can find in scopus, pubmed, etc.. Look also at this:

https://link.springer.com/article/10.1007/s00122-015-2497-x

http://www.transplantdb.eu/sites/transplantdb.eu/files/HandsOnTutorialtoGWAS_Seren-030715.pdf