My understanding is you plant many varieties in the field or greenhouse. You observe and measure for your desired traits. You genotype your entire population. This is where I am stuck.
How does phenotype observations + genotype sequences = molecular markers that we can one day use for marker assisted selection (MAS)?
How do I find molecular markers for desirable traits such as rhizomes, non shattering, and large seed size in wheat and sunflower?
Short answer to your question is: The strength of correlation/association between markers and traits enables identification of markers that may be used for MAS. You do not have to phenotype and genotype your 'entire' population. You can use a sample (of about 500-1000) genotypes that adequately capture the underlying variation in the population.
The following two documents (downloadable from RG) may help further understand what Dr Venkateswaran has aptly summarized.
Linkage Mapping and QTL Analysis
How realistic are the estimates of QTL parameters for assessing MAS eficiency?
It depends on the amount of work you are committed to invest. To find a particular marker, it is better to mine works of researchers who identified QTLs for your phenotype of interest. As one example for wheat seed size you can use the link to find markers tightly liked to genes controlling seed size.
https://www.crops.org/publications/cs/abstracts/54/1/98?access=0&view=pdf
Jacob,
Identification of marker for a desired trait requires two things, genotype data and phenotype data. Genotype data is converted into a genetic linkage map depending upon recombination frequencies between markers. This map can be obtained using MAPMAKER, MAP-MANAGER, JOINT-MAP etc.
Once the map is generated, we can identify marker-trait association using map data and phenotype data. This can be done using QTL-cartographer software. The closest marker can be used in MAS.
I would suggest you to read following article-
Collard B. C. Y. et al. (2005) Euphytica 142, pp 169-196
http://link.springer.com/article/10.1007%2Fs10681-005-1681-5
First you need reliable phenotypic info. It may be taken from no less than 300 individuals, either coming from a specific cross or a germplasm collection, replicated in time and space in order to adequately asses environmental variation and interactions.
Then you may use SNP markers or others. Association between markers and genes depend on the the density of the markers used, the higher the better. But redundant data, non informative markers and other considerations may make you reduce the number of markers to working set of about 10000.
Finally association bet ween markers and the desired characters will depend on your material, adequate grouping of the extremes of the character. Several grouping systems are used (see Pritchard ,2000). More related to potatoes in http://solcap.msu.edu/pdf%20files/6PAAextension.pdf
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