If I have kinship data, is population structure still needed when using the MLM? Or is only kinship, trait and genotype data needed?
Both the Q and K matrices should be included when running the MLM. If desired, you could compare the results of Q+K with that of the K-only model as well. When a marker is significant using the GLM but not when using the K matrix in MLM, this indicates that the association found under the GLM can also be explained by the relationships described by the K matrix. When you include both the Q and K matrices in your MLM, you have decided not to accept any marker-trait associations that can also be explained by either primary population structure (Q) or the general genetic background (K). 10.I have 30 marker loci (295 germplasm lines) but each loci has 2 alleles (differing in size). It seems that TASSEL considers the two alleles as different loci, thus accepting 60 loci instead of 30. Is there a way to fix this? A: TASSEL is in the process of fully supporting heterozygotes. 11.My population consists of outbred diploid individuals. The matrix that I generated using the KIN function in TASSEL
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- If I have kinship data, is population structure still needed when using the MLM? Or is only kinship, trait and genotype data needed?
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