I have performed GWAS for 1 rice population (300 genotypes) that were phenotyped at 3 locations for 2 continuous years. After GWAS, I am experiencing some issues, especially with the fine mapping to identify the causal SNPs. My issues: After running GWAS, I did not find any of the MTAs, that replicated either season-wise or location-wise results (GWAS results). So after the GWAS, I am not really sure how should I compile the results for the post-GWAS analysis to land on causal SNP. Any one can suggest how to fine map the SNPs to identify the causal SNP using PAINTOR or FINE MAP? I would be very thankful if your lab can assist me to solve this issue.
Looking forward to hearing from you soon.