TY - JOUR
T1 - SeedExtractor
T2 - An Open-Source GUI for Seed Image Analysis
AU - Zhu, Feiyu
AU - Paul, Puneet
AU - Hussain, Waseem
AU - Wallman, Kyle
AU - Dhatt, Balpreet K.
AU - Sandhu, Jaspreet
AU - Irvin, Larissa
AU - Morota, Gota
AU - Yu, Hongfeng
AU - Walia, Harkamal
N1 - Publisher Copyright:
© Copyright © 2021 Zhu, Paul, Hussain, Wallman, Dhatt, Sandhu, Irvin, Morota, Yu and Walia.
PY - 2021/2/1
Y1 - 2021/2/1
N2 - 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 s 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 used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates 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.
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 s 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 used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates 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.
KW - GWAS
KW - genome wide analysis
KW - image analysis
KW - rice
KW - seed color
KW - seed size
UR - http://www.scopus.com/inward/record.url?scp=85100856633&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85100856633&partnerID=8YFLogxK
U2 - 10.3389/fpls.2020.581546
DO - 10.3389/fpls.2020.581546
M3 - Article
C2 - 33597957
AN - SCOPUS:85100856633
SN - 1664-462X
VL - 11
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 581546
ER -