The foundation population consisted of mixture of various cultivars, inbred lines, breeding lines and F2s . Then, they were out-crossed using bees and underwent two cycles of recurrent selection for yield. After that, selected lines were selfed for two generations to fix alleles. The problem is that I don't have enough time to proceed to more generations of selfing and now I want to do QTL analysis for some yield and nutritional traits. what approach can be used for such population?
Thanks Alsamman, the challenge is that is population does not fit to common population types. i.e it is not biparental because its selection from outcrossing population. Also, its not multiparental e.g. MAGIC because we did not have control over the cross pollination events by bees. any ideas?
Even if your population is multiparental you must have biallelic markers that segregate in your offspring. You can use these markers to map QTLs.
You can see this paper :Assessing the complex architecture of polygenic traits in diverged yeast populations
where multiparental population is used for yeast
what is bothering about these lines is the unknown genetic recombination in the foundation population due to cross-pollination by bees, even we don't know the rate of outcrossing (0-~50%). I think there are two feasible approaches: 1. to consider lines as GWAS panel or 2. conducting deep sequencing of DNA pools from lines with extreme phenotype for the target trait and see allelic frequencies.
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