Therése Bengtsson

Background: Understanding the metabolic responses of wheat to drought stress is essential for developing strategies to enhance its resilience under water-deficit conditions. In this study, we investigated the metabolic and phenotypic responses of twelve Nordic spring wheat genotypes subjected to drought stress over 28 days in a high-throughput phenotyping facility. By integrating metabolic profiling with phenotypic assessments, we aimed to identify key metabolites and traits associated with drought tolerance. Results: We identified nearly 200 metabolites that were differentially accumulated across four time points, including early drought and recovery phases. Of these, 25% were organic acids, 16.2% sugars and derivatives, 16.2% amino acids and derivatives, and 10.4% alkaloids, while the rest were mainly lipids, nucleotides and derivatives, and phenolic acids. Furthermore, 32 metabolites showed significant correlations with 17 phenotypic traits, highlighting potential biomarkers for drought tolerance. These metabolic markers could be utilized in screening programs to accelerate the breeding of drought-resilient spring wheat. Our findings suggest that metabolomic changes during drought stress and recovery involve critical pathways linked to osmoprotection, antioxidant activity, and energy metabolism, which differentiate tolerant from non-tolerant genotypes. Conclusion: This study demonstrates the effectiveness of combining metabolomics with high-throughput phenotyping to dissect plant stress responses. By identifying key metabolic pathways and potential biomarkers for drought tolerance, our findings provide a valuable foundation for breeding climate-resilient wheat varieties. Moreover, this integrative approach enhances our understanding of plant adaptation to abiotic stress, contributing to future efforts in sustainable agriculture and food security.

Crown rust ( Puccinia coronata f. sp. Avenae Erikss.) poses a significant threat to oat production worldwide. The most effective strategy for managing this disease involves identifying, mapping, and deploying resistance genes to develop cultivars with enhanced resistance. In this study, we conducted a meta‐analysis of quantitative trait loci (QTLs) linked to crown rust resistance across diverse oat populations and environments. From 11 studies conducted between 2003 and 2024, we selected 167 QTLs, of which 127 were successfully mapped onto an oat consensus linkage map. These QTLs were mainly located on chromosomes of the D and C sub‐genomes, showing considerable variation in genetic distances and marker associations. Based on the integration of these QTLs in a meta‐QTL (MQTL) analysis, 23 MQTLs were identified for crown rust resistance in the oat genome. Gene mining within the MQTL intervals identified 1526 candidate genes, most of which were located in the D sub‐genome. Functional analysis revealed that these genes play key roles in stress response, hormonal regulation, and polyamine metabolism, which are crucial for plant defense. Conserved regulatory elements ( cis ‐acting regulatory element [CAREs]) were also identified in the promoter regions of key resistance genes, indicating their involvement in light response, stress regulation, and hormone signaling. This study represents a significant advancement in understanding the genetic architecture of crown rust resistance in oat and provides a valuable resource for breeding programs focused on improving disease resistance.

Elymus sensu stricto includes tetraploid species in the tribe Triticeae with a StH genome combination derived from Hordeum (H) and Pseudoroegneria (St). The group is related to many important cereals and forage grasses and is considered an important wild genetic resource for crop breeding. The relationships within Elymus s.s. have been difficult to resolve due to the large number of widely distributed species, a high degree of morphological diversity, introgression between species, and potential multiple origins. Using genome-wide DArTseqLD data from 57 taxa, including the StH group and associated species, it is possible to gain representative information about the genetic structure of the genus. SplitsTree, STRUCTURE and principal component analysis (PCoA) show that Elymus s.s. is divided into two major clades highly correlating with geographical origin separating American species from Eurasians. These findings, together with the contribution of different Pseudoroegneria and Hordeum species to the two clades, support the conclusion that Elymus s.s. has at least two independent origins. The Eurasian and American clades are further divided into three and two subclades, respectively. The results show that Elymus species have migrated multiple times from North to South America and between America and Eurasia. The new findings could be used to develop a new classification of Elymus s.s. with sections based on phylogenetic data.

Elymus mutabilis is a morphologically diverse species in the Poaceae family growing in Eurasia from northern Europe to far east Russia and southwards to central Asia. Elymus transbaicalensis occurs in similar habitats and is considered closely related to E. mutabilis and sometimes even referred to as a subspecies or synonym. Based on high similarity in morphology and habitat, molecular studies are needed to establish whether E. mutabilis and E. transbaicalensis can be considered as two distinct species. Thus, the objective of this study was to study diversity, relationships among populations and the phylogeographical structure of E. mutabilis and E. transbaicalensis using genotyping‐by‐sequencing (GBS). In total 68 individuals of E. mutabilis were sampled from 18 populations collected from northern Europe, central Asia and far east Russia, representing the central and two peripheral parts of the natural distribution of the species. The results reveal a clear distinction between E. mutabilis and E. transbaicalensis and no introgression. The phylogeographic structure of E. mutabilis follows the geographical distribution of the species. Populations from northern Europe, southern Siberia and far east Russia together form a clade separated from the peripheral populations in central Asia, indicating a common ancestry of the latter. Phylogenetic analyses revealed a radiation pattern among populations in northern Europe indicating a founding followed by rapid dispersal.

Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public–Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.

Cereal production in important growing regions is negatively influenced by climate change. This can be countered by expanding cereal production northwards in Scandinavia and Iceland, where today, barley (Hordeum vulgare L.) is primarily used as feed, as it rarely reaches malting quality. This study explores genetic factors underlying the ability of barley to mature fully in low temperature and long photoperiod. A panel of 84 spring barley lines were grown in controlled environments with different day lengths and temperatures, partially mimicking the target environment. The panel was screened for accumulated heat sum to heading, maturity, and height, all traits of importance for adaptation to the northern periphery. Subgroups with different stability and heat sum requirements were found, and day‐length‐neutral lines were identified. Height was temperature controlled, with lower temperature resulting in taller plants. The results were coupled to a genome‐wide association study (GWAS). Despite the small panel size, the Mat‐a locus was identified to have the strongest association with heat sum to heading; Ppd‐H1, Mat‐a, FT1, and DHAR2 with heat sum to maturity; and GA20ox1 with height. Early maturing lines with height stability have successfully been developed in Iceland, and this study confirms their performance in controlled environments for the first time. It provides insight to the mechanisms behind early maturity that will increase our ability to further adapt barley and other cereals to the northern climate. This will facilitate breeding work toward combining early maturity and height stability with traits such as quality, further enabling the northward expansion of grain production.

The discovery of novel resistance genes (R-genes) is an important component in disease resistance breeding. Nevertheless, R-gene identification from wild species and close relatives of plants is not only a difficult but also a cumbersome process. In this study, ResCap, a support vector machine-based high-throughput R-gene prediction and probe generation pipeline has been developed to generate probes from genomic datasets. ResCap contains two integral modules. The first module identifies the R-genes and R-gene like sequences under four categories containing different domains such as TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), Receptor-like kinase (RLK) and Receptor-like proteins (RLPs). The second module generates probes from extracted nucleotide sequences of resistance genes to conduct sequence capture (SeqCap) experiments. For the validation of ResCap pipeline, ResCap generated probes were synthesized and a sequence capture experiment was performed to capture expressed resistance genes among six spring barley genotypes. The developed ResCap pipeline in combination with the performed sequence capture experiment has shown to increase precision of R-gene identification while simultaneously allowing rapid gene validation including non-sequenced plants. The ResCap pipeline is available at http://rescap.ltj.slu.se/ResCap/ sandeep.kushwaha@slu.se or sandeep@niab.org.in Supplementary materials are available at Bioinformatics Advances online.

Blumeria graminis f. sp. hordei (Bgh), the causal agent of barley powdery mildew (PM), is one of the most important barley leaf diseases and is prevalent in most barley growing regions. Infection decreases grain quality and yields on average by 30%. Multi-parent advanced generation inter-cross (MAGIC) populations combine the advantages of bi-parental and association panels and offer the opportunity to incorporate exotic alleles into adapted material. Here, four barley MAGIC populations consisting of six to eight founders were tested for PM resistance in field trials in Denmark. Principle component and STRUCTURE analysis showed the populations were unstructured and genome-wide linkage disequilibrium (LD) decay varied between 14 and 38 Mbp. Genome-wide association studies (GWAS) identified 11 regions associated with PM resistance located on chromosomes 1H, 2H, 3H, 4H, 5H and 7H, of which three regions are putatively novel resistance quantitative trait locus/loci (QTL). For all regions high-confidence candidate genes were identified that are predicted to be involved in pathogen defense. Haplotype analysis of the significant SNPs revealed new allele combinations not present in the founders and associated with high resistance levels.