Rainfall regimes shape diversity in barley populations

Environmental factors have profound impact on seed development and maturation. It is known that temperature, water availability, and oxygen diffusion shape the physical properties of the seed coat and hormonal pathways that control dormancy and germination (Ali et al. 2021). Because crops are often exposed to both drought and flooding, understanding how local environmental conditions shape genetic diversity that affects seed traits and post-flood germination is not just academically interesting but is essential for improving agricultural resilience (Benech-Arnold et al. 2006). In the recent issue of Plant Physiology, Gómez-Álvarez and colleagues (2025) examine whether barley cultivars from regions with distinct rainfall amounts and patterns differ in genomic variations that determine whether barley seeds germinate after flooding. Using a georeferenced subset of landraces and wild relatives from the WHEALBI collection, the authors correlated a previously measured submergence-tolerance index (Gómez-Álvarez et al. 2023) with long-term precipitation variables extracted for each accession's collection site. Rainfall recorded at these sites during the driest month of the year and, to a lesser extent, during the warmest quarter correlated negatively with post-flood germination. Because all accessions were tested under identical germination conditions, precipitation does not directly influence germination performance in the assay. Instead, these associations indicate that long-term precipitation patterns at the sites of origin reflect the selective environments that have shaped genetic differences among accessions underlying variation in post-flood germination. Accessions from regions with drier summers germinated better after submergence than those from more humid regions. All environmental variables were obtained from the WorldClim2 database (Fick and Hijmans 2017), which provided consistent long-term precipitation data for each collection site. To uncover the genetic basis of this association, the authors performed an environmental genome-wide association studies (eGWAS) for submergence tolerance at germination using exome variants from the WHEALBI panel (Bustos-Korts et al. 2019; Caproni et al. 2023). A narrow region on chromosome 1 was identified as associated with differences in germination after flooding, supported by stringent multiple-testing thresholds and by the linkage disequilibrium structure of the broader collection. Within this interval, the authors identified 2 candidate genes whose haplotypes differed between accessions from the extremes of the rainfall distribution: HvDIR-like, encoding a dirigent-like protein implicated in lignin biosynthesis (Thamil et al. 2013), and HvSIN3-like, a transcriptional regulator associated with dormancy control through histone deacetylation (Wang et al. 2013). The haplotype groups denoted A (dry-origin) and B (more humid origin) displayed clear physiological differences when tested in soil after 4 days of flooding followed by 5 days of recovery. Haplotype A accessions reached substantially higher germination and seedling establishment (40% to 80%) than haplotype B accessions (0% to 25%), indicating that haplotype B accessions either remain more dormant or fail to resume growth after flooding. To understand the basis of the observed difference, Gómez-Álvarez and colleagues examined seed surface properties and dormancy-related traits. Fluorescence-lifetime imaging microscopy showed that haplotype B seeds had a “red-shifted” phasor distribution consistent with denser lignin, whereas haplotype A seeds displayed shorter lifetimes indicative of lighter lignification. HvDIR-like expression during late seed maturation was higher in haplotype B, consistent with reduced seed-coat permeability. These structural features likely restrict oxygen diffusion and water exchange during flooding, conditions known to promote dormancy under flood-induced hypoxia (Benech-Arnold et al. 2006). In parallel, the HvSIN3-like locus associates with differences in the ABA and GA balance that regulates dormancy (Ali et al. 2021). During submergence, haplotype B embryos showed higher HvSIN3-like transcript levels and increased expression of dormancy-related genes such as FUS3, ABI5, and NCED1, together with reduced CYP707A2 expression, which is involved in ABA catabolism. These transcriptional patterns, accompanied by elevated ABA content and induction of low-oxygen markers, align with secondary dormancy responses described previously (Liu et al. 2023). Treatment with nitric oxide donors, which are known to antagonize ABA-enforced dormancy, partially improved germination in haplotype B accessions, indicating a hormonal contribution to the observed differences (Mendiondo et al. 2016). Together, these results indicate that genetic variations associated with rainfall regimes are linked to differences in seed structure and dormancy behavior. HvDIR-like contributes to variations in seed coat properties, while HvSIN3-like modulates the hormonal control of dormancy. The combined effects of these alleles help explain why accessions originated from contrasting rainfall environments differ in their ability to germinate after flooding, connecting rainfall patterns with physiological outcomes (Fig. 1). A schematic model summarizing how genetic variations shaped by different rainfall regimes affect barley seed performance after flooding. Seeds from accessions originated from drier environments show lighter seed-coat lignification and lower dormancy, allowing efficient germination and seedling establishment after submergence. In contrast, seeds from accessions originating from humid regions exhibit denser seed-coat lignification and stronger ABA-dependent dormancy, resulting in reduced germination following flooding. Adapted from (Gómez-Álvarez et al. 2025), Supplementary Figure S9. The work by Gómez-Álvarez et al. (2025) provides an elegant demonstration of how natural rainfall variation can shape adaptive traits by selecting for genetic differences that influence seed germination behavior. Beyond its mechanistic insights, the study highlights the potential of environmental genomics for identifying allelic variants relevant to crop resilience. As rainfall becomes more unpredictable under climate change, clarifying how genetic variation linked to past precipitation patterns affects germination will be helpful for breeding cereals that can withstand both drought and flooding. In barley, long-term climate conditions have produced genetic variations that influence how seeds respond to submergence. Recent related articles in Plant Physiology: Rolletschek et al. (2024) reviewed the current knowledge on the role of low oxygen in seed development and germination In another review article, Holdsworth et al. (2024) discussed how geography, elevation, and agricultural contexts shape plant hypoxia responses, highlighting genotype–environment and population–genomic studies that connect environmental oxygen availability to variation in the oxygen-sensing pathway None. No new data were generated or analyzed in support of this research. All information needed to evaluate the study is contained within the article.