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6 markers on 200 plants = $1500; double the price if same analysis on 1000 plants
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The number of markers is the rub. You would need to work with at least 24 markers i.e. to sample for a round dozen traits with one marker on each side of the target gene region. This would mean quadrupling your stated price to $6000.
Since the same markers would have to be evaluated multiple times, the cost of marker evaluation would work out to about $36,000.00 to fix 12 traits.
I can see a pitfall of doing this and it must be something university work has already encountered. You would have to be able to pick out the best lines for future breeding work based on:
1. Which genes are closely positioned on the same chromosome.
2. Which plant contains more of the target genes
3. Which plant has the most target genes that are homozygous.
4. Which plant exhibits the best genetic envelope i.e. best package of non-target genes.
By selecting the best possible parents, the total cost of running the markers can be kept to a minimum. Poorly chosen parents could result in double the cost.
I should be able to write a program in Excel that would take most of the work out of the process. It would have to contain the entire tomato genome as a base and would have to be capable of estimating linkage values and determining the probability of crossovers. If we could evaluate multiple traits and then pick out the desirable variations, the total cost could be brought down significantly. In other words, it is more efficient to run markers for 12 traits than it is to run markers for a single trait looking for a single crossover event.
Thinking this through at a much higher level, this would need to be done with at least 100 total lines in order to develop a breeding population with sufficient variation. In other words, $17,000,000.00 just for running the markers in a big enough program. Lets say you needed to grow 1200 plants for each gene to be introgressed. This would infer a total of 14,400 plants that would have to be grown to select for 12 traits and by extension for 100 lines, would require 1,440,000 total plants.
This is purely speculative of course, but gives an idea of the scale a large program would entail.
DarJones