Integrative mapping in large inbred and hybrid association panels along with an F population advanced a novel understanding of general combining ability for plant height in maize.

We identified 44 QTL for PH-related traits evaluated for inbreds per se and GCA effects in large inbred and hybrid association panels and seven QTL for EH/PH in an F population coupled with BSA-seq. Among four co-localized QTL, seven novel potential candidate genes were significantly associated with PH-related traits, shedding new light on understanding the genetics of GCA for PH. Breeding optimal plant height (PH) is essential for improving maize (Zea mays L.) plant architecture, yield, lodging resistance, and density tolerance, yet there is limited genetic loci available regarding the general combining ability (GCA) for PH-related traits. In the current study, an inbred association panel of 312 inbred lines (IAP) along with a hybrid association panel (HAP) of 764 hybrid combinations were utilized to dissect the genetics of PH-related traits and their GCA effects across three environments. We found 44 quantitative trait loci (QTL) with 76 significant single-nucleotide polymorphisms (SNPs) for PH-related traits evaluated for inbreds per se and GCA effects; however, no overlapping loci were identified across inbreds per se and GCA effects, indicating conspicuous discrepancies in their genetics. In addition, GCA effects with complex genetic basis differed for diverse testers, which highlighted the specificity and complexity among heterotic groups. Correspondingly, we evaluated an F population derived from two parental lines LY-02 and LH513 with the contrasting EH/PH coupled with bulked segregant analysis by sequencing (BSA-seq) and found seven QTL for EH/PH. Among four co-localized loci across the association and QTL mapping, seven novel candidate genes were found to differently express among LY-02, LH513, and their F and were potentially associated with PH-related traits. The current study with combined mapping in diverse mapping populations provided a novel understanding of GCA for PH-related traits in maize.