Using SSR data in Tassel v5.0

[K.K.Vinod]

Hi,

I have a set of SSR marker data in which allele number per marker ranges from 2-4. Can I recode the alleles as A,T,G,C within each marker to simulate SNP variation, that can be analysed in Tassel v5.0?

Thanks and regards

Vinod

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[Peter Bradbury]

That sounds like it should work. One thing to watch for with multi-allelic data is that you are more likely to end up small genotype class sizes than with bi-allelic data. For MLM or GLM, I would not trust a significant test for a site if one of the genotype class sizes is less than 5 and if that is the genotype class with the largest effect size as outliers can have a major effect. You can check that by looking at the allele effect estimates for significant sites. I prefer to see genotype class sizes of 10 or greater.

Peter

[K.K.Vinod]

Thanks Peter,

I will try making the genotype class size of less than 10 as null. Thanks for your comments.

Regards

Vinod

Dr K K Vinod, M Sc (Ag), PhD, DCPA
Senior Scientist (Plant Breeding)

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INDIAN AGRICULTURAL RESEARCH INSTITUTE
Rice Breeding and Genetics Research Centre
Aduthurai 612101
Tanjavur District
Tamil Nadu
INDIA

 

E-mail: kkvi...@gmail.com, kkv...@iari.res.in

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[Kalyani Kulkarni]

Dear Sir

Greetings

In conversation to the above said, for each SSR marker, if it has four alleles, each allele should be A, B, C, D respectively in the input data file, 

the name of the SSR marker will be repeated in the column four times?