SeedExtractor: an Open-Source GUI for Seed Image Analysis

Accurate measurement of seed size parameters is essential for both: breeding efforts□aimed at□enhancing yields and basic research□focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that□determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 seconds for analyzing an image, i.e. significantly less compared to the other tools. As this software is open-source, it can be modified by users□to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were subjected to genome-wide association analysis. We identified well-known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrated the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. HIGHLIGHT SeedExtractor is an open-source application designed to accurately measure seed size and seed color in a time-efficient manner for a wide variety of plant species.