Hello Team,

I am running a GWAS analysis on a diploid plant with FarmCPU and I got result with no significant SNPs ( See attached QQ plots of RED & GREEN ). I would like to know how can I improve the P threshold value by using FarmCPU ? Details o f my GWAS study is below :
The phenotype is the color of the fruits-.I.e: the intensity of each color channel ( RED, GREEN & BLUE ) is used as the phenotype.

1. The following QC steps has done before GWAS : --geno 0.1, --maf 0.1, --hwe 1e-6 and --indep-pairwise 500 50 0.95 (plink used for QC filter)
2. Total number of SNPs Before QC steps : 4951441
3. Total number of SNPs after QC steps : 794861
4. Total Number of Samples : 183
5. Top3 PCs are used as Covariates.

6. FarmCPU commad Used :

   myFarmCPU<-FarmCPU(Y=myY[,c(1,2)],CV=myCV,GD=myGD,GM=myGM,MAF.calculate=TRUE,maf.threshold=0,QTN.threshold = 0.01,method.bin="optimum",bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),threshold.output=1,maxLoop=30

Please somebody can suggest me that is there any optimization way for improving P threshold Value ?