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RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture

by Chen, Yunyu , Chang, Yongyue , Yang, Wanneng , Shi, Jiawei , Wang, Xin , Lou, Qiaojun , Xie, Shangyuan , Wang, Jianglin , Li, Weikun

in Accuracy / Algorithms / Automation / biotechnology / computer software / cost effectiveness / Crops / Cultivars / Deep learning / dissection / Drought / drought tolerance / Droughts / Efficiency / Gene mapping / genes / high‐throughput phenotyping platform / Inbreeding / Methods / Oryza - anatomy & histology / Oryza - genetics / Oryza - physiology / Phenotype / Phenotyping / Plant Breeding / Plant Roots - anatomy & histology / Plant Roots - genetics / Quantitative trait loci / Quantitative Trait Loci - genetics / quantitative traits / Rice / rice drought resistance / root phenotyping / root system architecture / root systems / Roots / Software / water stress

2025

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RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture

by Chen, Yunyu , Chang, Yongyue , Yang, Wanneng , Shi, Jiawei , Wang, Xin , Lou, Qiaojun , Xie, Shangyuan , Wang, Jianglin , Li, Weikun

2025

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RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture

by Chen, Yunyu , Chang, Yongyue , Yang, Wanneng , Shi, Jiawei , Wang, Xin , Lou, Qiaojun , Xie, Shangyuan , Wang, Jianglin , Li, Weikun

2025

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Journal Article

RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture

Chen, Yunyu,

Chang, Yongyue,

Yang, Wanneng,

Shi, Jiawei,

Wang, Xin,

Lou, Qiaojun,

Xie, Shangyuan,

Wang, Jianglin,

Li, Weikun

2025

Overview

Summary The dissection of genetic architecture for rice root system is largely dependent on phenotyping techniques, and high‐throughput root phenotyping poses a great challenge. In this study, we established a cost‐effective root phenotyping platform capable of analysing 1680 root samples within 2 h. To efficiently process a large number of root images, we developed the root phenotyping toolbox (RPT) with an enhanced SegFormer algorithm and used it for root segmentation and root phenotypic traits. Based on this root phenotyping platform and RPT, we screened 18 candidate (quantitative trait loci) QTL regions from 219 rice recombinant inbred lines under drought stress and validated the drought‐resistant functions of gene OsIAA8 identified from these QTL regions. This study confirmed that RPT exhibited a great application potential for processing images with various sources and for mining stress‐resistance genes of rice cultivars. Our developed root phenotyping platform and RPT software significantly improved high‐throughput root phenotyping efficiency, allowing for large‐scale root trait analysis, which will promote the genetic architecture improvement of drought‐resistant cultivars and crop breeding research in the future.

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Publisher

John Wiley & Sons, Inc,John Wiley and Sons Inc

Subject

/ Crops