Hey, I think that you just have to know the right places to look. I started with ArrayExpress, one of the greatest data-hosting websites, and have already found numerous eQTL studies on crops / agriculture:
- eqtl-Identification of expression QTL of ABA response in sunflower
- EXPRESSION QTL MAPPING ACROSS SOIL MOISTURE ENVIRONMENTS REVEALS CONTRASTING ASSOCIATIONS WITH GENOMIC FEATURES IN ARABIDOPSIS THALIANA
- Transcription profiling by array of barley parental and near-isogenic lines in response to Puccinia hordei infection
There were more than those which I have posted here. Hopefully each study does indeed provide both the expression and genotyping data.