ELMERF: A deep-learning-assisted hydroponic RGB phenotyping framework for rice seedling salt-stress evaluation and genetic mapping.

Abstract

Rice seedling salt-tolerance evaluation commonly relies on visual scoring or destructive assays, which are subjective, labor-intensive, and difficult to standardize for population-level analysis. This study developed a new deep-learning-assisted hydroponic RGB phenotyping framework for standardized salt-stress evaluation and genetic mapping in rice seedlings. The framework integrates controlled hydroponic cultivation, RGB imaging, RicePhenoSeg-assisted annotation and trait extraction, ELMERF-based semantic segmentation, and image-derived quantification of salt-induced shoot injury. Using this framework, we constructed the Rice Seedling-Salt RGB Dataset (RSSD), which contains green shoot tissues, yellow shoot tissues, roots, and background from hydroponically grown rice seedlings. Based on RSSD, ELMERF achieved a mean Intersection over Union of 51.4% and a mean Accuracy of 89.5%, outperforming nine representative segmentation models. We further defined shoot yellowing rate (SYR) as an image-derived quantitative trait describing visible salt-induced shoot injury. The framework was applied to 261 re-sequenced rice accessions for population-level phenotyping and genome-wide association analysis. Compared with standard evaluation score and seedling death rate, SYR showed a more continuous phenotypic distribution and detected 36 significant SNPs, including a major signal near the Saltol/OsHKT1; 5 region. Notably, 34 SYR-associated SNPs were not detected by conventional visual scores. Overall, this study provides a targeted hydroponic RGB phenotyping framework for standardized rice seedling salt-stress evaluation and genetic analysis.

Plant phenotyping relevance

深層学習によるRGB画像セグメンテーション、形質抽出、データセット構築、性能比較を中核とし、画像由来の塩ストレス傷害形質を定量化する植物フェノタイピング手法である。

Code and data availability

The paper's Data Availability statement explicitly deposits datasets, source code, and supporting data in a public GitHub repository (ELMERF), which covers the RSSD RGB image dataset, segmentation code, and phenotyping/GWAS analysis assets. RiceVarMap is a cited external SNP database, not a paper-specific asset.