Association mapping

[Vanina Castroagudin]

Deal all,

Looking for some help here, I am working with a pop of rust fungi separated in subgroups based on SNPs data. Do any of you know if it is possible to do some kind of association mapping test in Poppr2 and the calculate X2 value for each marker, to see which marker has more contribution to each group?

All ideas about how to figure this out in other ways are also welcome.

Thanks,

Vanina Castroagudin

[Zhian Kamvar]

Not sure about the association mapping, but you can use the results from DAPC to pull out the loci that contribute to the observed differentiation

see https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-dapc.pdf and https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html

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