QTG-Miner aides the rapid cloning of quantitative trait gene and dissection of co-directional selection of tassel branch number in maize. Zea mays

We developed a multi-omics data based technique QTG-Miner driven by machine learning algorithms for the large-scale and rapid cloning of QTGs in maize. Using QTG-Miner, we cloned and verified seven functional genes underlying seven TBN QTLs. Compared with conventional methods, QTG-Miner showed robust for both major and marginal-effect TBN QTLs. Interestingly, co-directional selection signatures were significantly enriched in multiple biological pathways between the female heterotic groups (FHGs) and male heterotic groups (MHGs) during modern hybrid maize breeding. In summary, QTG-Miner provides a novel large-scale approach for QTG rapid cloning in crops and sheds light on the genetic basis of TBN for further maize breeding.