First, evolution, genetics and ecology are distinct subjects: you're not going to find any one textbook that covers all these subject areas in the depth that you are looking for. Even within the field of genetics, which would cover your preliminary interests in epistasis and heritability, I would recommend that you start with two or three textbooks that you can then cross-reference to get a different point-of-view, perspective, and explanation. All of them cover PCR at an introductory level, but not RT-PCR and diagnostic gene chips.
I don't know of any text that goes into the depth of genotype X environment interaction effects (GxE) that you want because this subject crosses over into numerous other fields, including psychology and the health sciences. Quantitative traits (QST) and molecular markers (FST) can also get very specialized, then you're getting into genetic linkages and DNA sequencing - advanced genetics.
You're definitely much more into the realm of genetics than either evolution or ecology if your'e focussing on QTL, GxE, Fst/Qst, RT-PCR and gene chips, but you'd still have to narrow down what you want to learn as no textbook will cover all these subjects indepth. You'll probably just have to get a good introductory text and do some independent research into your specific field(s) of interest.
Some good intro genetics texts are:
"Genetics: Analyses of Genes and Genomes," by Hartl and Jones (covers QTL, maternal heritability, and PCR)
"Genetics: From Genes to Genomes," by Leland Hartwell, Leroy Hood, Michael L. Goldberg, Lee M. Silver, Ruth C. Veres, Ann Reynolds.
"Concepts of Genetics," by William S. Klug, Michael R. Cummings.
"Essential iGenetics," by Peter J. Russell (not the best)
You can get good reviews on these books through Amazon.com or another option is to go to the college bookstores in your area and browze through the textbooks that are currently being used for specific courses in genetics.
