Dear All,

Please forgive my ignorance I am new to association studies. Please provide me with some comments and insight on what I would like to achieve.

Main goal

I have genotyped 100+ individuals for 40 SNP makers and would like to associate a genotype with particular phenotypic trait etc.

Phenotypes

1. I have several phenotype traits I would like to associate a genotype with.
2. The individuals are also group into different class based on several phenotype observations. What I have read so far is that I can add phenotypic trait to a phenotype file to be used with plink. With regards to the groups do I treat each group as a "phenotype" and also add these to the phenotype file I will be using with plink.

Results

What I would like to achieve in the end is for each group a representative genotype. Would this be possible any help would be appreciated, if possible examples of ped,map and pheno files would also be appreciated as this is what I am aslo unsure of as to how to represent this is the different files.

Thanks

I do believe I am not expressing myself clearly I apologies. The 40SNPs that have been chosen have been associated with the phenotypes/traits in previous studies (published) so the association to the phenotype/trait does indeed exist. I would like to determine if a specific SNP call ( A/G or A/C ) has a effect on the trait/phenotype.

Example:

These are just to explain what I would like to achieve and not real cases.

Using on 2 markers for this example and 8 plants (same species).

Marker 1: associated with flower colour

Marker 2: associated with plant height

• Plant 1 Flower colour: Red
• Plant 2 Flower colour: Yellow
• Plant 3 Flower colour: Red

• Plant 4 Flower colour: Yellow

• Plant 1 height : 60cm (classified as tall)

• Plant 2 height : 45cm (classified as average)
• Plant 3 height : 52cm (classified as average)
• Plant 4 height : 62cm (classified as tall)

So results for

Plant    Marker 1    Maker 2
1        A/A         C/A
2        A/T         C/T
3        A/A         C/T
4        A/T         C/A

Given the example results if a seedling of a plant is test for bother markers and Marker 1 is A/A is could be hypothesized that it will have red flowers and Marker 2 is C/T it would be of average height.

I do hope this helps.