Using SSR data in Tassel v5.0

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K.K.Vinod

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Jul 23, 2014, 8:07:25 AM7/23/14
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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

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Jul 24, 2014, 12:07:37 PM7/24/14
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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

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Jul 25, 2014, 6:13:14 AM7/25/14
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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 VinodM Sc (Ag), PhD, DCPA
Senior Scie
ntist (Plant Breeding)

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Kalyani Kulkarni

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Mar 29, 2021, 6:15:46 AM3/29/21
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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? 

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