The new challenges of plant breeding urge to integrate the latest innovations in biology and genetics to enhance crop improvement. QTL analysis fills the gap between "omics" and the field. Since most cloned QTLs are elements involved in gene regulation, the candidate approach, comparing the position of plant phenotype QTLs, gene expression QTLs (eQTLs) and network eQTLs may increase our chances to clone QTLs of agronomic traits. This vertical integration of information needs the availability of fixed segregant populations. Recombinant inbred line populations constitute a valuable experimental design for this purpose because (1) their mapping resolution (important to distinguish between linkage from pleiot-ropy) and (2) they facilitate the study of epistasis. Epistatic QTLs are frequently missed when using other experimental designs.
QTL meta-analysis is a horizontal way to integrate information for the same trait from different experiments, populations (better if they are connected through com-
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