Hi,
I have phenotypic data for disease scoring (1-5) over three years for 184 cacao lines. The scoring was done in single environment over a period of three years. To calculate the mean, do I just average the score in excel or I shall calculate BLUPs? I want to perform GWAS analysis to look disease resistance QTLs.
If it were a single year data with biological replicates for given genotype, I would perform GWAS with mean values. As you have data for multiple year, I would recommend using linear unbiased prediction of genotypic effect (year fixed effect and genotype random effect) as phenotypic value for GWAS. Your response to the query will be valuable @Boby Mathew
Your scoring was done at same location for three year (this indicates three environments; as you wrote single envirnment, that not true), You should use BLUP values for GWAS analysis.
I also think you should use BLUPs for GWAS.
If you ever want to compute a mean, do not use excel !!! Use your favorite statistical software (like R) : it will be faster and you will reduce computations mistakes.
You should use BLUP values for GWAS. That may give accurate results.
Asis Shrestha , clearly I would recommend the use of BLUPs, but why do you recommend to consider the "year" effect as a fixed effect? In some papers, I saw that both genotypic and year effects have to be considered as random... I wonder why here the effect of the year is fixed?
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