Identification of Indica–Japonica Attributes and Analysis of Heterosis Using InDel Markers

With the development and improvement of indica–japonica hybrid rice breeding technologies, it has become possible to directly utilize the heterosis between indica and japonica subspecies to cultivate high-yielding rice varieties. Precisely analyzing the attributes and heterosis levels of indica–japonica varieties is crucial for successfully breeding indica–japonica hybrid rice and utilizing heterosis. This study employed 34 insertion–deletion (InDel) molecular markers to identify the indica–japonica attributes in 122 rice varieties and validated the results using cluster analyses and principal component analyses (PCAs). Additionally, the yield-related traits of the hybrids and parents were assessed, heterosis was analyzed, and the feasibility of predicting heterosis using parental genetic distance (GD) was explored. InDel molecular markers showed that all the hybrids were indica–japonica crosses with varying genetic components, confirmed by the cluster analyses and the PCAs. A heterosis analysis revealed that an increase in the effective panicle number per plant (EP) was the main factor in increasing the yield. Different GD intervals showed varying correlations with trait heterosis. These results indicate the effectiveness of InDel molecular markers in accurately distinguishing indica–japonica attributes and that hybrid combinations demonstrate significant heterosis. This study provides a reference for parent selection and utilizing heterosis in indica–japonica hybrid rice.