GWASpoly use in a mixed ploidy population

[ctkach7]

Hi Dr. Endelman,
Thank you for the GWASpoly R package, it has already been very helpful in my GWAS analysis in switchgrass (Panicum virgatum).
Will GWASpoly be able to process a mixed population of diploids and tetraploids at the same time?
If not, do you have any recommendations for the best way to proceed with a GWAS analysis for this mixed population?

The population of switchgrass that I am working with is a mixture of approximately 250 allotetraploids and 250 octoploids. Following the instructions in the manual for polyRAD I have been able to obtain within a single VCF file both diploid and tetraploid genotype calls.

The P.virgatum_v5 reference genome [Panicum virgatum genome assembly P.virgatum_v5 - NCBI - NLM (nih.gov)] was created from an allotetraploid switchgrass accession. Following the advice within the polyRAD manual the allotetraploid individuals in my population had SNP markers genotyped as diploid markers and the octoploid individuals in my population had SNP markers genotyped as tetraploid markers.

Thank you for your time and advice, it is greatly appreciated!
Chris Tkach

[jendelman]

Good question! It is possible to analyze a mixed ploidy population with GWASpoly under the assumption that the genetic architecture is unaffected by ploidy. (We are conducting research to go beyond this assumption and hope to share more in 2024.)
My recommendation for now is as follows:

1. Code marker data based on the highest ploidy. For example, for a mixture of 2x and 4x individuals, the (0,1,2) coding for 2x individuals becomes (0,2,4).
2. Include ploidy as a cofactor in the model.

Let me know how it works for you!

Jeff