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Background  Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F 1  hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments.    Results  A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z 1  and Z 2  populations was six and eight, respectively. Notably, all the eight environmentally stable QTLs for Z 2  were characterized by overdominance effect (OD), suggesting that overdominant QTLs were the most important contributors to heterosis for PH and EH. Furthermore, 14 environmentally stable QTLs were anchored on six genomic regions, among which four are trait-specific QTLs, suggesting that the genetic basis for PH and EH is partially different. Additionally,  qPH.A-1.3 , modifying about 10 centimeters of PH, was further validated in backcross populations.    Conclusions  The genetic basis for PH and EH is partially different, and overdominant QTLs are important factors for heterosis of PH and EH. A major QTL  qPH.A-1.3  may be a desired target for genetic improvement of maize plant height.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-017-0503-9) contains supplementary material, which is available to authorized users.

Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III