Screening of Wheat Varieties Under Combined Low Temperature and Waterlogging Stress Based on Physiological Phenotyping and Transcriptome

Compound low‐temperature and waterlogging events frequently co‐occur during the wheat ( Triticum aestivum L.) jointing stage. Still, cultivar ranking and the trait dimensions that discriminate tolerance under this compound stress remain poorly resolved because most studies consider each stress in isolation. Here, we screened 30 wheat cultivars under four treatments: normal water and temperature (NN), waterlogging at normal temperature (WN), normal water at low temperature (NL) and waterlogging at low temperature (WL). At jointing, potted plants were exposed outdoors in open‐top chambers (OTCs; day/night 15/−4°C) and/or waterlogging for 10 days, after which 26 physiological, biochemical and root anatomical indices were quantified (including chlorophyll fluorescence, relative electrical conductivity, TTC‐based root activity and root morphological traits) and yield components were determined at maturity. Integrating standardized indicators using principal component analysis, a membership function and clustering separated cultivars into four tolerance groups, identifying JM22 as highly tolerant and LY615 as highly sensitive. Across the panel, WL imposed the most potent inhibition of photosynthetic performance, root function and grain yield, exceeding the effects of WN or NL alone. Consistent with this ranking, JM22 maintained higher PSII efficiency and root activity under WL, accompanied by stronger induction of stress‐responsive, photosynthesis‐related gene sets. Root transcriptome analysis further indicated shared activation of phenylpropanoid biosynthesis in both cultivars, whereas differential regulation of plastid/photochemistry‐associated and nitrogen‐metabolism pathways distinguished tolerant versus sensitive responses. Together, these results provide a trait‐and‐transcript framework for identifying germplasm and prioritizing candidate processes for breeding and management in environments prone to concurrent cold and waterlogging.