Image based analysis of plants is a high-throughput and non-invasive approach to study plant traits. Based on plant image data, the quantitative estimation of many plant traits (leaf area index, biomass etc.) is associated with accurate segmentation of individual leaves. However, this task is challenging due to the presence of overlapped leaves and lack of discernible boundaries between them. In addition, variability in leaf shapes and arrangement among different plant species limits the broad utilisation of current leaf instance segmentation algorithms. In this paper, we propose a novel framework that relies on under-segmentation of plant image using a graph based formulation to extract leaf shape knowledge for the task of leaf instance segmentation. These shape priors are generated based on leaf shape characteristics independent of plant species. We demonstrate the performance of the proposed framework across multiple plant dataset i.e. Arabidopsis, Komatsuna and Salad. Experimental results indicate its broad utility.