We are going to do QTL mapping in biparental population, the population was genotyped with the SNP markers with (already known physical location). so my question is that do we need to carry out linkage mapping to proceed for qtl mapping ( marker trait associaiton) ?
Yes, because even you know the physical positions of SNP markers you need to know significant marker trait association (MTA), for that you can use TASSEL-GLM or MLM model.
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Yes. Linkage and physical maps are different even though both shows the position of markers on chromosomes. Linkage map is different because it shows the position on chromosomes based on recombination frequency.
Hi, Kashmiri. Yes, using a linkage map as reference for classical QTL mapping is essential. Certainly, in a same species, most of the linkage positions and the physical positions are highly correlated. However, we should not ignore the mutations present across cultivars/accessions/origins. We, hence, should always map the QTL in the same mapping population. Besides, this also explains why one reference genome is no longer enough and agriculture research communities are moving towards pangenomics now. Like other colleagues' comments, linkage mapping takes recombination frequency between markers or marker and trait as basis, unlike GWAS. There are pros and cons between GWAS and linkage methods. We experienced 40% markers cannot be mapped using GWAS in oil palm because of unknown physical positions, but we managed to salvage most of these markers by improving the reference genome based on multiple linkage maps. This is always good for having linkage maps around, especially for non-model species. Hope this helps, Kashmiri.
