I think there are a number of studies on antimalarial drug resistance that would fulfil your criteria. See e.g. the seminal paper on artemisinin resistance: http://www.nature.com/nature/journal/v505/n7481/full/nature12876.html

The gene was identified in an in-vitro screen of a resistant parasite line, then is was shown in Cambodian field isolates that mutations in the gene are associated with delayed parasite clearance.

Just look into any book of classical genetics (Morgan, Sturtevant, McClintock, etc.) Those guys figured out the genetics of many traits long before the demonstration that the DNA was the inheritable material.

Hope this helps.

House mouse nest building: looked at by many people, but then studied in the wild by Carol Lynch

I published an article about environmental adaptation in Drosophila where we generated an hypothesis about the possible phenotypic outcome of a naturally occurring mutation and then we tested our hypothesis using wild-derived populations... Not sure if it fits your demand... but it is worth trying ;-) 

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004560

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

Abstract

The increase in availability of whole genome sequences makes it possible to search for evidence of adaptation at an unprecedented scale. Despite recent progress, our understanding of the adaptive process is still very limited due to the difficulties in linking adaptive mutations to their phenotypic effects. In this study, we integrated different levels of biological information to pinpoint the ecologically relevant fitness effects and the underlying molecular and biochemical mechanisms of a putatively adaptive TE insertion in Drosophila melanogaster: the pogo transposon FBti0019627. We showed that other than being incorporated into Kmn1 transcript, FBti0019627 insertion also affects the polyadenylation signal choice of CG11699 gene. Consequently, only the short 3′UTR transcript of CG11699 gene is produced and the expression level of this gene is higher in flies with the insertion. Our results indicated that increased CG11699 expression leads to xenobiotic stress resistance through increased ALDH-III activity: flies with FBti0019627 insertion showed increased survival rate in response to benzaldehyde, a natural xenobiotic, and to carbofuran, a synthetic insecticide. Although differences in survival rate between flies with and without the insertion were not always significant, when they were, they were consistent with FBti0019627 mediating resistance to xenobiotics. Taken together, our results provide a plausible explanation for the increase in frequency of FBti0019627 in natural populations of D. melanogaster and add to the limited number of examples in which a natural genetic mutation has been linked to its ecologically relevant phenotype. Furthermore, the widespread distribution of TEs across the tree of life and conservation of stress response pathways across organisms make our results relevant not only for Drosophila, but for other organisms as well.

There are plenty of examples of such traits from Arabidopsis and other plants. People have figured out the genetic basis of these traits using classical genetics and or QTL-mapping in the lab. Just to name a few traits Flowering time, trichome production, seed dormancy (I've done some work on seed dormancy myself). And then variation in these traits has been investigated in wild populations.

In general, it seems that only a subset of genes that affect a certain trait, like flowering time, are variable in wild populations. There are several reviews of this topic.

in gene mapping studies...linkage mapping is a more way reliable way to find new genes as compare to association mapping in wild population...So any research article related to marker based cloning or linkage mapping of gene may be answer your interest.

This occurs almost routinely in forest genetic field trials, for instance with respect to damage caused by both biotic and abiotic stresses.  Such damage can be characteristic and often comes to notice in common-garden experiments where it can be scored and quantitative inheritance of susceptibility/resistance studied from data analysis.  I have encountered that personally with Pinus radiata.

Such field (or nursery or even greehouse) data will not of itself elucidate anything about specific genes being involved, but it can certainly provide a platform for that when supplemented by good genomic data.

The first circadian clock gene, period (per), was identified in Drosophila by Benzer in 1971. Following that, the genetics of the circadian clock was studied extensively in the lab, but only 20 years later, in the 90's, Costa and Kyriacou started looking on natural genetic variation of the the per gene in wild populations of Drosophila. The same applies for the timeless genes that was first studied in the lab (mid 90's) and only 10 years later was analysed in wild populations.