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

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Plant Biotechnology Journal Pub Date : 2025-03-13 DOI:10.1111/pbi.70040

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

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引用次数: 0

Abstract

SummaryThe 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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RPT：用于分割和量化根系结构的综合根系表型工具箱

水稻根系遗传结构的解剖在很大程度上依赖于表型分析技术，而高通量的根系表型分析是一个巨大的挑战。在这项研究中，我们建立了一个具有成本效益的根系表型平台，能够在2小时内分析1680个根系样本。为了高效地处理大量根系图像，我们开发了带有增强的SegFormer算法的根系表型工具箱（RPT），并将其用于根系分割和根系表型特征。基于该根系表型平台和RPT，从219个水稻重组自交系中筛选了干旱胁迫下的18个候选QTL区域（数量性状位点），验证了这些QTL区域鉴定的OsIAA8基因的抗旱功能。该研究证实了RPT在处理各种来源的图像和挖掘水稻品种抗逆性基因方面具有很大的应用潜力。我们开发的根系表型分析平台和RPT软件显著提高了高通量根系表型分析效率，实现了大规模的根系性状分析，这将促进未来抗旱品种遗传结构的改进和作物育种研究。

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来源期刊

Plant Biotechnology Journal 生物-生物工程与应用微生物

CiteScore

20.50

自引率

2.90%

发文量

201

审稿时长

1 months

期刊介绍： Plant Biotechnology Journal aspires to publish original research and insightful reviews of high impact, authored by prominent researchers in applied plant science. The journal places a special emphasis on molecular plant sciences and their practical applications through plant biotechnology. Our goal is to establish a platform for showcasing significant advances in the field, encompassing curiosity-driven studies with potential applications, strategic research in plant biotechnology, scientific analysis of crucial issues for the beneficial utilization of plant sciences, and assessments of the performance of plant biotechnology products in practical applications.