Imbibitional damage and germination kinetics reveal genetically distinct components of cold sensitivity in soybean seeds

Abstract Background Reliable crop establishment under early sowing is a key objective for soybean adaptation to cooler European environments. Low temperatures during germination can impair establishment through chilling-induced imbibitional damage during early water uptake and delay germination under continuous cold conditions. However, whether these responses share a genetic basis remains unclear. We phenotyped an early-maturity soybean diversity panel from the EUCLEG collection under control and cold conditions using a set of 25 phenotypic descriptors that captured seedling emergence, timing, uniformity and extent of germination in seed populations. Results Cold imbibition during the initial phase of water uptake increased imbibitional damage, resulting in reduced germination and impaired seedling growth. Modelling germination kinetics using multiple time-to-event and logistic regression-derived parameters provided a detailed characterization of the genetic architecture underlying seed germination at different temperatures. Germination kinetics displayed a temporally structured genetic architecture, with loci associated with early germinators differing from those associated with late germinators such as time to 70–80% germination. Germination kinetics at 20 °C and 10 °C were largely controlled by distinct loci, suggesting temperature-dependent genetic control of germination speed. Likewise, loci associated with relative temperature responses of germination speed differed from those detected at a single temperature, indicating a specific genetic basis for temperature sensitivity. Accessions that were highly sensitive to chilling-induced imbibitional damage were not necessarily those showing the strongest delay in germination under continuous exposure to 10 °C. Consistent with this phenotypic uncoupling, loci associated with imbibitional damage did not overlap with those controlling germination kinetics. Candidate genes located near significant markers were related to hormonal signalling, oxidative stress responses, membrane-associated processes, and cell-wall modification. Conclusions Our results show that cold sensitivity during early establishment involves distinct physiological and genetic components. Chilling-induced imbibitional damage and delayed germination under continuous low temperature were phenotypically and genetically uncoupled, suggesting that improving one trait may not improve the other. Modelling germination as a population-based process revealed a time-dependent genetic architecture underlying seed responses to cold. These findings highlight the importance of complementary phenotyping approaches and identify genomic regions that support breeding for improved soybean establishment under cool sowing conditions.