Background: Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results.Results: Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance.Conclusions: Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.

Increased precipitation during winter months in Western Europe is predicted from climate change. This is expected to increase the frequency of flooding events, with waterlogged conditions becoming more prevalent. A consequence of waterlogging is hypoxic conditions and dying back of roots, thereby negatively affecting plant nutrient uptake, growth, and development. Barley (Hordeum vulgare L.) forms lysigenous aerenchyma, which are air‐filled pockets within the root to facilitate O₂ transport and support root respiration. Current methods for visualizing aerenchyma formation in roots are largely 2D and involve embedding a fixed root segment in resin, followed by destructive sectioning for microscopy. Here, we report the development of an X‐ray computed tomography (CT) acquisition and analytical method for spatio‐temporal identification and quantitation of aerenchyma in 2D and 3D in barley roots without the requirement for chemical fixation, resin embedding, followed by physical sectioning of the root. We demonstrated that the method we have developed can facilitate the identification and quantitation of aerenchyma in barley as early as 9 d post‐waterlogging. The method we have developed can be potentially applied to different plant species and has the potential to support the selection of breeding markers through X‐ray CT phenotyping of aerenchyma.

Picea sitchensis, Sitka spruce, is of interest to forestry as both a conservation species and a highly productive crop. Its native range stretches from Alaska to California, and it is hence distributed across a large environmental cline with areas of local adaptation. The IUFRO collection, established in 1968–1970, consists of 81 provenances of commercial and scientific interest spanning this native range. We used genotyping-by-sequencing on 1177 genotypes, originating from 80 of the IUFRO provenances which occupy 19 geographic regions of the Pacific Northwest, resulting in an SNP database of 36,567 markers. We detected low levels of genetic differentiation across this broad environmental cline, in agreement with other studies. However, we discovered island effects on geographically distant populations, such as those on Haida Gwaii and Kodiak Island. Using glaciation data, alongside this database, we see apparent post-glacial recolonization of the mainland from islands and the south of the range. Genotyping the IUFRO population expands upon the use of the collection in three ways: (i) providing information to breeders on genetic diversity which can be implemented into breeding programs, optimizing genetic gain for important traits; (ii) serving a scientific resource for studying spruce species; and (iii) utilizing provenances in breeding programs which are more tolerant to climate change.

Alnus glutinosa (L.) Gaertn (also known as common alder and black alder) is an important broadleaf species in Europe, valued for its ecological functions in riparian ecosystems and its versatile hardwood timber. Despite its importance, natural regeneration and productivity have declined due to habitat fragmentation and the spread of the pathogen Phytophthora alni. To support a sustainable supply of improved planting material, a national breeding programme was established in Ireland. In this study, we evaluated growth traits of 80 half-sib families derived from 103 selected plus-trees under field conditions and applied genome-wide single nucleotide polymorphism (SNP) markers to assess genetic diversity and perform genomic prediction of growth performance. The progeny trial revealed considerable variation in height and diameter-at-breast-height (DBH), with heritability estimates ranging from 0.45 to 0.53 for relative growth in height, and from 0.28 to 0.31 for DBH across different periods. Genotyping-by-sequencing (GBS) of 103 plus-trees genotyped identified 95,139 SNP markers, revealing high genetic diversity and no evidence of inbreeding, confirming the broad genetic base of the Irish breeding population. Genomic prediction using genome-wide markers provided low-to-moderate predictive ability for height and negligible predictive ability for DBH, reflecting the limitation of small training population size and relatedness. However, the markers demonstrated immediate value for diversity monitoring and seed orchard management. These findings identify superior A. glutinosa genotypes and provide a genomic framework for improving existing seed orchards and supporting sustainable forestry through enhanced A. glutinosa breeding.

Sitka spruce (Picea sitchensis (Bong.) Carr.) is the dominant plantation conifer in Atlantic Europe, yet the genomic basis of provenance-level climate adaptation remains poorly resolved. We applied gradient forest analysis to 31,049 genome-wide SNPs from 1106 individual trees representing 79 native-range provenances in the IUFRO collection, using three environmental predictors retained after collinearity screening: Longitude, Temperature Seasonality, and Annual Precipitation. Longitude was the dominant driver of genomic turnover (mean R² = 0.01168), followed by Temperature Seasonality (0.00672) and Annual Precipitation (0.00228), reflecting the long-distance coastal gradient of the native range. A redundancy analysis conditioned on ancestry principal components confirmed a significant multivariate genotype–environment association (F = 8.679, p = 0.001). Genomic offset was negatively correlated with all three provenance-level performance traits measured at the IUFRO common garden after 50 years of growth: height, stem diameter and stem quality, providing empirical validation of the genomic-climatic framework. Projecting the fitted model onto European planting sites using an 8-GCM CMIP6 ensemble showed mean offset increasing from 0.0021 (SSP2-4.5, 2041–2060) to 0.0041 (SSP5-8.5, 2061–2080), with the most climate-exposed cells under the high-emission late-century scenario approaching the upper tail of the source population offset distribution. The European planting region showed a higher projected offset than the North American source range under all scenarios. This supports the hypothesis that provenances from Oregon to southern British Columbia are most suited for planting in regions under future Atlantic European conditions.