“…If the same eQTL is found for several genes, a so‐called ‘hot‐spot’, this locus is likely to harbour a master regulator (Breitling et al ., ). Additionally, as the differences in gene expression underlie many phenotypic and physiological differences between genotypes, QTLs can be shared between genes and other quantitative traits (Fu et al ., ; van Zanten et al ., ; Burow et al ., ; Kerwin et al ., , ; Joosen et al ., ; He et al ., ; Jimenez‐Gomez, ; Jensen et al ., ,b). Moreover when gene expression is measured in multiple populations, plant stages, tissues or environments, the variation in these traits can be placed in a gene‐by‐environment context.…”