Hello everyone,

I am currently using an F2 population created by crossing plant varieties with dark colors and those with light colors to search for genes related to color intensity.

I performed RNA-seq, extracted SNPs from the data to create a VCF file, and conducted a GWAS, but I'm struggling to interpret the results. Specifically, I performed the GWAS using “SPAD values,” “chlorophyll a,” “chlorophyll b,” and “chlorophyll a + chlorophyll b” values, but no SNPs showing a significant -log10(P) value were detected for any of them. However, regarding chlorophyll, an interesting peak appeared on a specific chromosome, though the -log10(P) value wasn't very high. We found that the function of the gene associated with this SNP seems to be related to chloroplasts.

My question is: How should the threshold for -log10(P) be set in GWAS analysis? Should we include these as candidate genes even if they are not statistically significant?

We are currently using -log10(P)=5.

The peaks under discussion are 3 and 5.

I would appreciate your ideas.