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Teacher questions are one of the crucial components in developing students’ concept maps in project-based learning (PjBL). The study aims to measure the quality of students’ concept maps and determine the PjBL stages that accommodate concept map quality using an expanded teacher question. This research was a quasi-experiment with 335 students as participants from five senior high schools. To collect the data, teachers used open questions during the PjBL learning process with three categories: main, standard, and expanded teacher questions. The concept map data were collected from students of Biology. The student’s concept map score is calculated based on the achievement of the experts’ Concept map. Data were analyzed using Manova. The results showed that teacher questions in the PjBL stage increased the concept map component scores, especially in valid relationships and crosslink, while other components increased, no effect, and decreased. The most influential PjBL stage that accommodates concept map quality improvement is the deciding stage. Hence, our findings supported that the deciding stage of PjBL is the primary stage to improve the quality of students’ thinking. The expanded teacher’s questions in the study group, the way of collecting data, and the data analysis significantly contributed to the improvement in the quality of students’ thinking.
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