qPH_1.01, a dominant QTL that contributes to plant height and ear height in maize

Plant height (PH) is an important agronomic trait closely related to yield and lodging resistance. In this study, bulked segregant analysis coupled with next-generation sequencing (BSA-seq) approach was employed to identify quantitative trait loci (QTLs) for PH in a large F₂ population generated from a cross between the tall maize (Zea mays L.) inbred line PH6WC and the short maize inbred line KA3321. Extreme high- and low-PH bulks were constructed by selecting 62 individuals each from the tails of the phenotypic distribution in the 617-member F₂ population.  BSA-seq revealed four PH QTLs, two of which were validated in a random F₂ population. qPH_1.01, a novel QTL on chromosome 1, showed dominance effect for reducing both PH and ear height (EH). The KA3321 allele of qPH_1.01 reduced PH by 8-12 cm and EH by 4-6 cm. Using recombinant-derived progeny testing strategy, qPH_1.01 was fine-mapped to an interval of approximately 420 kb referring to B73 genome. Transcriptome data showed that qPH_1.01 might influence PH and EH by regulating expression of hormone-related genes. The dominant QTL discovered in this study may facilitate the breeding of dwarf and high-density maize varieties.