7 parental lines were crossed using diallel mating technique, I now have 21 F1 and 21F1 reciprocals and 21 F2 and 21F2 reciprocals. The objectives of the study are to investigate the morphological and molecular traits associated with seed yield in the soybean genotypes, to evaluate QTLs conditioning seed yield and its components in the soybean genotypes, and to investigate the consistency of the QTLs associated with seed yield and its components across the soybean genotypes.
In general, qtl analysis should be done through the software like qtl cartographer. I don't think that there will be any lab, who will help with only qtl mapping, unless there is a collaboration. Try with this software. It is user friendly.
A lot depends on your crop and population within the crop (inbred vs. outcrossing; diploid vs. polyploid; level of genetic variability; etc.).
QTL analysis (ignoring association studies, as they require even larger populations...) is typically conducted with a fairly large segregating population with a defined population structure. Neither 21 F1s (assuming segregating F1s resulting from crossing two highly-heterozygous parents) nor 21 F2s would represent enough recombination events to even generate a decent linkage map, much less detect QTL effects.
I suggest that you research QTL anaylysis software (MapQTL, QTLCartographer, MultiQTL, etc.) and see what kinds of populations they support. Read some literature on QTL analysis (I recommend Collard and Mackill, 2005 [linked], although I am sure there are some more recent pubs that are as good or better) to get an idea of the population size and number of markers that are required for the level of resolution and power to detect QTL that you need for your experiment. Then, you should design your experiment accordingly.
After properly designing the experiment you can look into labs to genotype your population for you.
Article An introduction to markers, quantitative trait loci (QTL) ma...
I guess you want to do genotyping with SSR or SNP markers? I can recommend you to send samples to Laboratory of Plant Genetics and Evolution, Hokkaido University, Japan (Dr. Jun Abe). They have large collection of soybean SSR markers. I can help you to contact them.
Regarding QTL mapping analysis, as other mentioned, there are plenty of QTL mapping softwares (MapQTL, QTL Cartographer, IciMapping). MapQTL and QTL Cartorapher are widely known, while IciMapping is a convenient software that combines linkage map construction and QTL mapping.
Best regards,Maria
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