Existence of abiotic stress-responsive genes within the regions of QTLs controlling maize grain yield: One of the root causes for unstability of the QTLs?

•Dissection of genes within the maize quantitative trait loci is difficult.•Why do the QTLs have a considerable variance in natural environments?•We conducted co-localization of QTLs and stress-responsive genes on chromosomes.•The stress-responsive genes are likely important gene components of maize QTLs.•The stress-responsive genes are one of root causes for unstability of the QTLs.

Dissection of functional genes within the quantitative trait loci (QTLs) controlling maize yield is typically labor intensive and has placed determinants for further utilization of QTLs to breed maize because of no direct and simple strategies to identify the genes. Additionally, considerable variance of the QTLs with the environmental conditions in practice has, for a long time, been less understood at the level of the gene expression. A large-scale co-localization of 94 QTLs controlling yield and 1433 abiotic stress-responsive genes on chromosomes in maize together with 74 genes non-responsive to the abiotic stresses as controls was conducted. Consequently, 383 (40.8%) of 938 water deficit-regulated genes, 70 (23.6%) of 296 salt stress-regulated genes and 40 (20%) of 199 Al-toxicity stress-regulated genes were projected on regions of the QTLs, respectively. In conclusion, the abiotic stress-responsive genes are likely important gene components of maize QTLs and their conditional expression thereby lead to unstability of the QTLs with changes in environmental conditions. Our results give informative clues to clone and identify the gene components within the QTLs although some ideas proposed in this study further require experimental verification in future.