Are landraces from inbred crop ? If so F2 population can be most informative population for mapping. F2 population is genetically very informative. But F2 is different from RILs in respect to dominance as this consists of high frequency of heterozygotes. Major challenge is phenotyping- unless your crop is clonally propagated - you can not replicate F2 plants. For very low heritability traits like yield this may be very challenging but for high heritability traits like maturity or disease resistance you can accurately phenotype. It is always important to accurately phenotype to get good QTL mapping results. 

Hi Konoutan,

What you describe is done quite frequently, not only with landraces but organisms from natural populations; e.g. the large body of research in the Mimulus guttatus complex, Arabidopsis lyrata, and Boechera stricta to name just a few examples.  Usually the objective involves understanding the genetic basis and structuring of differences between divergent populations or varieties.

There are two related considerations to keep in mind.  First, unless the varieties are highly inbred, crossing different parents from the two landraces, or even using  different F1 individuals from the same parental cross might result in different QTLs segregating.  Thus, it's difficult to know if your results can be generalized to the starting varieties without some replication using different parents.

Second, and more basic, is being clear about what your objectives are.  Do you want to understand the basis for phenotypic differences between divergent landraces or the broader populations they represent, or simply use the landraces as samples of within-species variation?  In the first case, the results can provide a lot of insight on the nature of the genetic differences, even without actually finding the underlying genes, provided the results are robust across different crosses.  In the second case, it's questionable what you can really infer beyond the simple existence of QTLs with effects large enough to detect, which is seldom an interesting question these days.

Off course you can go for local cultivars, but it should be highly polymorphic for the trait u r targeting and  basically landraces or local cultivars will have more undesirable alleles along with target trait so it's better to develop either NILs or RILs...As F2 mapping population is not eternal

Yes, It does. Of course.

The principal issue is that the parental segragate for some traits that you want study. If not, you can not obtain genomic regions associated with your trait of interest.

Best wishes

Hi Konoutan,

Yes, landrace can be used as parent for QTL mapping. However you should be cautious about homogeneity of the landrace. Parents should be highly homozygous. Since landraces many times show heterogeneity, you need to make selection to obtain it in homogeneous form before going for actual crossing to get mapping population.

One more thing, immortal lines such as RILs and DHs are preferred for QTL mapping because they produce true-breeding lines or homozygous lines that can be multiplied or reproduce without genetic changes occurring. This allows conduct of replicated trials at different locations/year/environments. This is very much needed when your target trait is polygenic, governed by QTL.

Hope this will help you, I assume you are working on self pollinated crop.

Best wishes,

Thank you all for your answers. Mr Ravindra I am working on pearl millet (Pennisetum glaucum) which is a cross-pollinated species.

Yes, Its possible.  landrace can be used as parent for QTL mapping.

For outcrossing species, you don't have to develop inbred lines and in some cases you can't; e.g. if the plants are self incompatible or if there are issues with inbreeding depression.  Outcross F2 designs can be used, in which two different crosses between the two landraces or populations are made, using different parents, and F1s from each parental cross are crossed to generate the F2.  Segregation patterns both for markers and QTLs can be more complex, but there are techniques for dealing with this.   See, for one of many examples, Leinonen et al. 2013 (Molecular Ecology 22:709-723).

Even if pearl millet can be inbred, and I gather it can from some of the literature I've seen, the outbred F2 design might be desirable since you sample multiple alleles from each landrace and get a better idea of whether the variation between landraces is consistent.  Or, you can use a normal inbred design but replicate it with multiple crosses.

Yes that is true but some when we will select the landracese in that time we should have the Inbred lines to know bout the trait because  some time a single trait will governed by the multiple QTLs . 

I think it is OK, especially when the two landraces owns different traits of which you are focusing on