In many crops the genomes have sequenced and plenty of markers are available for most of the important traits. Is it possible to develop a high yielding variety having all desirable quality traits coupled with resistance/tolerance to important biotic and abiotic stresses?
yes it is possible to develop such cultivars in most of the field crops but hard in case of trees. If the markers are linked to desirable traits closely and one takes in account besides foreground selection background selection as well. Linkage drag is also be kept in mind
In theory yes it is possible, but in practice it will not be easy as we do not know enough about all of the available alleles of all if the genes, and their interactions with each other (dominance for alleles at a single locus, and epistasis for alleles at different loci), with genetic background, and the environment.
Nope. for several reasons:
1) what you consider as "perfect" will not be so for others.
2) going from the sequence information on genes to breeding value is far from straightforward.
3) QTL markers point to variation *in the mapping population*. Another mapping population would probably have identified different QTLs.
4) assembling all favourable genes in a single genotype requires many generations of crossing.
5) as regards pest and disease resistance the best variery of today is not necessarily the best variety of tomorrow. Pathogens adapt.
So, with genome sequence, markers for all important traits and MAS, you make a decisive step toward developing better varieties, faster. Search for the "perfect variety" is however an illusion.
A genotype is more or less adapted to a given environment. An intensive cultivar usually is depressed under drought conditions. A stable-yielding cultivar will not compensate for large inputs, etc. Except predictable environmental factors (soil, latitude), there are unpredictable. So I think that there are no perfect varieties but growers need to have a system of complementary varieties. Actually, gene interactions, genotype - environment interaction, and coenotic nature of many important traits (they arise at coenotic level only and cannot be reduced to lower levels of material organization) make MAS for complex traits much more complicated then it is sometimes advertised.
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