Combining cost-effective germination imaging and genome-wide association study to unravel genetic variation of temporal salinity responses in wheat

doi:10.1016/j.jia.2026.02.010

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Qing Li¹^*, Zhuangzhuang Sun²^*, Xiaofang Li³^*, Zihan Jing¹, Xiaomiao Tian⁴, Yinchen Zhang³, Yingyin Yao⁴, Zhen Zhang⁵, Meng Wang⁶, Xiao Wang¹, Qin Zhou¹, Jian Cai¹, Yingxin Zhong¹, Mei Huang¹, Wenliang Wan³^#, Jiawei Chen¹^#, Dong Jiang^1,^2,³^#

¹National Technique lnnovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture and Rural Affairs/College of Agriculture, Nanjing Agriculture University, Nanjing 210095. China

²School of Agronomy, Anhui Agricultural University, Hefei 230036, China

³Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China

⁴Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China

⁵State Key Laboratory of Crop Stress Adaptation and Improvement/The Zhongzhou Laboratory for Integrative Biology/College of Agriculture, School of Life Sciences, Henan University, Kaifeng 475004, China

⁶State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 211135, China

Highlights

l A cost-effective germination phenotyping system for facilitating in situ monitoring of the dynamic germination responses was established.

l A deep learning pipeline to achieve organ segmentation and germination-related trait extraction processes was developed.

l Substantial germination variation in salt sensitivity among wheat varieties was identified, showing no correlation between germination capacity and seed size, and radicle growth rate significantly exceeding that of the coleoptile.

l 429 loci associated with salt stress response during germination were detected.

Abstract
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摘要

盐胁迫是制约全球小麦生产的关键因素，尤其是在种子萌发阶段影响显著。传统萌发期耐盐性评价方法通量低，且难以捕捉动态表型变化。本研究整合侧视RGB成像与图像分析算法，构建了一套低成本、高通量的种子萌发表型鉴定平台，并利用深度学习算法实现了器官级别的小麦萌发图像分割与萌发相关性状的精准提取，进而对多个小麦品种在不同盐浓度下的萌发动态进行系统表型解析。研究表明，器官级分割模型表现优异：平均精确率达89.08%，平均召回率91.65%，像素准确率91.65%，平均交并比（mIoU）83.20%；所提取的13项图像衍生性状与人工测量结果高度一致。该研究揭示了盐胁迫显著抑制根系与幼苗的生长，且抑制效应随盐浓度升高而增强，发现了胚根生长速率显著快于胚芽鞘，但种子大小与其萌发能力无显著相关性。基于动态图像提取指标开展的聚类分析将210份小麦材料划分为盐耐受性差异显著的两类。全基因组关联分析（GWAS）共鉴定出429个与萌发期盐胁迫响应显著相关的遗传位点，其中包含一个已被报道参与植物耐盐调控机制的潜在候选基因 TraesCS7A03G007080。综上，本研究不仅为小麦萌发期耐盐品种筛选提供了重要遗传和表型资源，同时建立了一套低成本、高通量、高可靠性的技术体系，为深入解析小麦萌发期耐盐性的遗传基础提供了有力支撑。

Abstract

Salt stress is a major limiting factor for global wheat production, especially during the germination stage. Traditional methods for evaluating salt resistance at the germination stage are limited by low throughput and their inability to capture dynamic phenotypic changes. In this study, a low-cost and high-throughput seed germination phenotyping platform was developed by integrating side-view RGB imaging with image analysis algorithms. Organ segmentation and germination related traits extraction processes was built via a deep learning pipeline for comprehensive phenotyping of the germination process of diverse varieties under different salt levels. Organ-level segmentation achieved a mean precision of 89.08%, a mean recall of 91.65%, a pixel accuracy of 91.65%, and a mean intersection over union of 83.20%. The 13 image-derived traits were highly consistent with manual measurements. Salt stress significantly inhibited the growth of roots and seedlings, with inhibitory effects intensifying as salt concentration increased. Further analysis revealed seed size shows no correlation with germination capacity and radicle growth rate significantly surpasses that of the coleoptile. Clustering analysis based on dynamic image-derived indices classified the 210 wheat materials into two groups with significantly different salt tolerance. GWAS identified 429 loci associated with salt stress response during germination, including one potential candidate gene, TraesCS7A03G007080, known to play a role in salt tolerance mechanisms. This study provides important genetic materials for the evaluation of salt-tolerant wheat varieties at the germination stage and offers a low-cost, high-throughput, and reliable technical approach for dissecting the genetic basis of salt tolerance during wheat germination.

Keywords: wheat germination salinity stress high-throughput phenotyping GWAS

Online: 05 February 2026

Fund:

This research was supported by the projects of the National Key Research and Development Program of China (2024YFD2301305), the Natural Science Foundation of Jiangsu Province, China (BK20241543), the Jiangsu Innovation Support Program for International Science and Technology Cooperation Project, China (BZ2023049), the Key R&D Project of Shandong Province, China (2024TZXD070), the National Natural Science Foundation of China (32502036, 32272213, 32030076, U1803235, 32021004), the National Key Research and Development Program of China (2023YFD2300200), the China Agriculture Research System (CARS-03), the Shandong Province First-class Discipline Construction “811” Project, China, and the Jiangsu Collaborative Innovation Center for Modern Crop Production, China (JCIC-MCP).

About author: #Correspondence Wenliang Wan, E-mail: Wanwl@shzu.edu.cn; Jiawei Chen, E-mail: chenjiawei@njau.edu.cn; Dong Jiang, E-mail: jiangd@njau.edu.cn # These authors contributed equally to this work.

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Qing Li, Zhuangzhuang Sun, Xiaofang Li, Zihan Jing, Xiaomiao Tian, Yinchen Zhang, Yingyin Yao, Zhen Zhang, Meng Wang, Xiao Wang, Qin Zhou, Jian Cai, Yingxin Zhong, Mei Huang, Wenliang Wan, Jiawei Chen, Dong Jiang. 2026. Combining cost-effective germination imaging and genome-wide association study to unravel genetic variation of temporal salinity responses in wheat. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.02.010

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