[Help] TASSEL MLM GWAS results showing zero output

[Dr. Md. Farhad (Nabin)]

Dear TASSEL Users,

I am running a GWAS in TASSEL using the MLM model, but my output table shows zero SNP effect estimates. I searched through documentation and online discussions, but I could not pinpoint the issue.

Some details about my dataset:

Number of genotypes: 164

Model used: MLM with PC covariates

Error message/log: “Number of rows: 0” in the Allele Estimates table

I came across suggestions that this could happen if the phenotype does not have enough variation. Could that be the case? If so, what strategies can I use to proceed with my dataset? Also, is 164 genotypes too small for TASSEL MLM to detect associations?

I would greatly appreciate it if anyone could provide guidance or share similar experiences.

Thank you very much for your time and support.

Best regards,
Md. Farhad

[Muhammad Atif Wahid]

i think you should calculate kinhsip and add population Q in your Q matrix.....for SNP markers you should use Tassel 5.0

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[Jasdeep Kaur]

Hello Everyone!

I have used TASSEL V5 for SSR markers analysis but my professors are asking me to use TASSEL V4 for these SSR markers. Is there any difference between the both.  

Please let me know. 

Thanks and Regards 

Jasdeep Kaur

 PhD Scholar

 Department of Vegetable Science and Floriculture 

CSK Himachal Pradesh Krishi Vishvavidyalaya Palampur, 176062 

Himachal Pradesh, India

To view this discussion visit https://groups.google.com/d/msgid/tassel/CACq1Qvn7o7UY025h7Pp1ynyYHKEeEpDvTjo_H%2BD8aH7FQOAiYg%40mail.gmail.com.

[Brandon Monier]

Hi Jasdeep,

TASSEL 5 is designed around nucleotide-based data (e.g., VCF, HapMap, etc.). TASSEL 4 is tailored for SSR data, but you can still use v5 for SSR data import.

From the FAQ (https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load):

Can I import non-nucleotide data, such as SSR data, into TASSEL?

Yes. To import non-nucleotide data into TASSEL 5.x, alleles should be recoded using the nucleotide symbols (A,C,G,T,+,-) in diploid hapmap format. Doing so provides a way to import chromosome and position for each site. If any site has more than 6 alleles, only the five most common alleles should be coded separately and the remaining alleles should be pooled together as ‘-‘. Alternatively code each allele as a separate site with each allele in turn coded as A and any other allele coded as C. Numeric values for the data can be imported into TASSEL 4.x using the polymorphism format described in the TASSEL 3 User Guide. Warning: it is the users responsibility to make sure that any subsequent analysis is appropriate for their data. Some TASSEL methods, such as LD and Association Analysis, are best suited for bi-allelic data. For example, LD analysis pools only minor alleles into a single class, thus forcing all data to be bi-allelic prior to analysis.

Best,

Brandon M.