RT Journal Article
SR Electronic
T1 <em>SeedExtractor</em>: an open-source GUI for seed image analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.28.176230
DO 10.1101/2020.06.28.176230
A1 Feiyu Zhu
A1 Puneet Paul
A1 Waseem Hussain
A1 Kyle Wallman
A1 Balpreet K Dhatt
A1 Jaspreet Sandhu
A1 Larissa Irvin
A1 Gota Morota
A1 Hongfeng Yu
A1 Harkamal Walia
YR 2020
UL http://biorxiv.org/content/early/2020/06/29/2020.06.28.176230.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.