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Background  Root systems play important roles in crop growth and stress responses. Although genetic mechanism of root traits in maize ( Zea mays  L.) has been investigated in different mapping populations, root traits have rarely been utilized in breeding programs. Elucidation of the genetic basis of maize root traits and, more importantly, their connection to other agronomic trait(s), such as grain yield, may facilitate root trait manipulation and maize germplasm improvement. In this study, we analyzed genome-wide genetic loci for maize seedling root traits at three time-points after seed germination to identify chromosomal regions responsible for both seedling root traits and other agronomic traits in a recombinant inbred line (RIL) population (Zong3 × Yu87–1).    Results  Eight seedling root traits were examined at 4, 9, and 14 days after seed germination, and thirty-six putative quantitative trait loci (QTLs), accounting for 9.0–23.2% of the phenotypic variation in root traits, were detected. Co-localization of root trait QTLs was observed at, but not between, the three time-points. We identified strong or moderate correlations between root traits controlled by each co-localized QTL region. Furthermore, we identified an overlap in the QTL locations of seedling root traits examined here and six other traits reported previously in the same RIL population, including grain yield-related traits, plant height-related traits, and traits in relation to stress responses. Maize chromosomal bins 1.02–1.03, 1.07, 2.06–2.07, 5.05, 7.02–7.03, 9.04, and 10.06 were identified QTL hotspots for three or four more traits in addition to seedling root traits.    Conclusions  Our identification of co-localization of root trait QTLs at, but not between, each of the three time-points suggests that maize seedling root traits are regulated by different sets of pleiotropic-effect QTLs at different developmental stages. Furthermore, the identification of QTL hotspots suggests the genetic association of seedling root traits with several other traits and reveals maize chromosomal regions valuable for marker-assisted selection to improve root systems and other agronomic traits simultaneously.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1383-5) contains supplementary material, which is available to authorized users.

Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize