Genome-wide association study reveals 18 QTL for major agronomic traits in a Nordic-Baltic spring wheat germplasm.

Spring wheat (Triticum aestivum L.) remains an important alternative to winter wheat cultivation at Northern latitudes due to high risk of overwintering or delayed sowing of winter wheat. We studied nine major agronomic traits in a set of 299 spring wheat genotypes in trials across 12-year-site combinations in Lithuania, Latvia, Estonia, and Norway for three consecutive years. The dataset analyzed here consisted of previously published phenotypic data collected in 2021 and 2022, supplemented with additional phenotypic data from the 2023 field season collected in this study. We combined these phenotypic datasets with previously published genotypic data generated using a 25K single nucleotide polymorphism (SNP) array that yielded 18,467 markers with a minor allele frequency above 0.05. Analysis of these datasets via genome-wide association study revealed 18 consistent quantitative trait loci (QTL) replicated in two or more trials that explained more than 5% of phenotypic variance for plant height, grain protein content, thousand kernel weight, or heading date. The most consistent markers across the tested environments were detected for plant height, thousand kernel weight, and days to heading in eight, five, and six trials, respectively. No beneficial effect of the semi-dwarfing alleles Rht-B1b and Rht-D1b on grain yield performance was observed across the 12 tested trials. Moreover, the cultivars carrying these alleles were low yielding in general. Based on principal component analysis, wheat genotypes developed in the Northern European region clustered separately from those developed at the southern latitudes, and markers associated with the clustering were identified. Important phenotypic traits, such as grain yield, days to heading, grain protein content, and thousand kernel weight were associated with this clustering of the genotype sets. Interestingly, despite being adapted to the Nordic environment, genotypes in the Northern set demonstrated lower grain yield performance across all tested environments. The results indicate that spring wheat germplasm harbors valuable QTL/alleles, and the identified trait-marker associations might be useful in improving Nordic-Baltic spring wheat germplasm under global warming conditions.

Deacclimation and reacclimation processes in winter wheat: novel perspectives from time-series transcriptome analysis.

Winter wheat achieves freezing tolerance (FT) through cold acclimation (CA) - a process which is induced by low positive temperatures in autumn. The increasing occurrences of temperature fluctuations in winter lead to deacclimation (DEA), causing premature loss of FT, and the cultivars capable of reacclimation (REA) are more likely to survive the subsequent cold spells. The genetic mechanisms of DEA and REA remain poorly understood, necessitating further research to bolster climate resilience in winter wheat. Here, we selected two winter wheat genotypes with contrasting levels of FT and conducted a ten-week-long experiment imitating low-temperature fluctuations after CA under controlled conditions. Crown and leaf tissue samples for RNA-sequencing were collected at CA, DEA, and REA time-points. It is the first transcriptomic study covering both short- and long-term responses to DEA and REA in winter wheat. The study provides novel knowledge regarding CA, DEA, and REA and discusses the gene expression patterns conferring FT under temperature fluctuations. The freezing-tolerant genotype "Lakaja DS" showed elevated photosynthetic activity in leaf tissue and upregulated cryoprotective protein-encoding genes in crowns after CA when compared to the freezing-susceptible "KWS Ferrum". "Lakaja DS" also expressed cold acclimation-associated transcripts at a significantly higher level after 1 week of DEA. Following REA, "Lakaja DS" continued to upregulate dehydrin-related genes in crowns and exhibited significantly higher expression of chitinase transcripts in leaves, when compared to "KWS Ferrum". The findings of this study shed light on the genetic mechanisms governing DEA and REA in winter wheat, thus addressing the gaps in knowledge regarding FT under low-temperature fluctuations. The identified genes should be further examined as potential molecular markers for breeding strategies focused on developing freezing-tolerant winter-type crops. Publicly available datasets generated in this study are valuable resources for further research into DEA and REA, contributing towards the enhancement of winter wheat under global climate change.

Genome-wide association analysis identifies a consistent QTL for powdery mildew resistance on chromosome 3A in Nordic and Baltic spring wheat.

KEY MESSAGE: QPm.NOBAL-3A is an important QTL providing robust adult plant powdery mildew resistance in Nordic and Baltic spring wheat, aiding sustainable crop protection and breeding. Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, poses a significant threat to bread wheat (Triticum aestivum L.), one of the world's most crucial cereal crops. Enhancing cultivar resistance against this devastating disease requires a comprehensive understanding of the genetic basis of powdery mildew resistance. In this study, we performed a genome-wide association study (GWAS) using extensive field trial data from multiple environments across Estonia, Latvia, Lithuania, and Norway. The study involved a diverse panel of recent wheat cultivars and breeding lines sourced from the Baltic region and Norway. We identified a major quantitative trait locus (QTL) on chromosome 3A, designated as QPm.NOBAL-3A, which consistently conferred high resistance to powdery mildew across various environments and countries. Furthermore, the consistency of the QTL haplotype effect was validated using an independent Norwegian spring wheat panel. Subsequent greenhouse seedling inoculations with 15 representative powdery mildew isolates on a subset of the GWAS panel indicated that this QTL provides adult plant resistance and is likely of race non-specific nature. Moreover, we developed and validated KASP markers for QPm.NOBAL-3A tailored for use in breeding. These findings provide a critical foundation for marker-assisted selection in breeding programs aimed at pyramiding resistance QTL/genes to achieve durable and broad-spectrum resistance against powdery mildew.

Genome-Wide Association Analysis of Freezing Tolerance and Winter Hardiness in Winter Wheat of Nordic Origin.

Climate change and global food security efforts are driving the need for adaptable crops in higher latitude temperate regions. To achieve this, traits linked with winter hardiness must be introduced in winter-type crops. Here, we evaluated the freezing tolerance (FT) of a panel of 160 winter wheat genotypes of Nordic origin under controlled conditions and compared the data with the winter hardiness of 74 of these genotypes from a total of five field trials at two locations in Norway. Germplasm with high FT was identified, and significant differences in FT were detected based on country of origin, release years, and culton type. FT measurements under controlled conditions significantly correlated with overwintering survival scores in the field (r ≤ 0.61) and were shown to be a reliable complementary high-throughput method for FT evaluation. Genome-wide association studies (GWAS) revealed five single nucleotide polymorphism (SNP) markers associated with FT under controlled conditions mapped to chromosomes 2A, 2B, 5A, 5B, and 7A. Field trials yielded 11 significant SNP markers located within or near genes, mapped to chromosomes 2B, 3B, 4A, 5B, 6B, and 7D. Candidate genes identified in this study can be introduced into the breeding programs of winter wheat in the Nordic region.

Comparative Analysis of Antioxidant Accumulation under Cold Acclimation, Deacclimation and Reacclimation in Winter Wheat.

Low temperature during cold acclimation (CA) leads to the accumulation of detrimental reactive oxygen species (ROS) in plant tissues, which are scavenged by antioxidants, such as ascorbate and glutathione. However, there is a lack of studies examining the dynamics of antioxidants throughout CA, deacclimation (DEA), and reacclimation (REA) in winter wheat. Six winter wheat genotypes were selected to assess the effect of CA, DEA, and REA on the concentrations of ascorbate and glutathione in leaf and crown tissues under two CA temperature treatments. Higher levels of total, reduced, and oxidised ascorbate were determined in leaves, whereas crowns accumulated higher concentrations of nicotinamide adenine dinucleotide (NAD+) after CA, DEA, and REA. Constant low temperature (CLT) during CA led to higher contents of ascorbate and glutathione in both tissues at all stages of acclimation, in comparison with prolonged higher low temperature (PHLT). The concentrations of antioxidants increased after CA, tended to decrease after DEA, and returned to CA levels after REA. Significant positive correlations between freezing tolerance (FT) and antioxidants were only determined under the CA at CLT treatment, thus, affirming the negative effect of PHLT during CA on the FT of winter wheat.

The effect of cold acclimation, deacclimation and reacclimation on metabolite profiles and freezing tolerance in winter wheat.

Global climate change will cause longer and warmer autumns, thus negatively affecting the quality of cold acclimation (CA) and reducing the freezing tolerance (FT) of winter wheat. Insufficient FT and fluctuating temperatures during winter can accelerate the deacclimation (DEA) process, whereas reacclimation (REA) is possible only while the vernalization requirement is unfulfilled. Six winter wheat genotypes with different winter hardiness profiles were used to evaluate the impact of constant low-temperature (2°C) and prolonged higher low-temperature (28 days at 10°C followed by 2°C until day 49) on shoot biomass and metabolite accumulation patterns in leaf and crown tissues throughout 49 days of CA, 7 days of DEA, and 14 days of REA. The FT of winter wheat was determined as LT30 values by conducting freezing tests after CA, DEA, and REA. Shoot biomass accumulation, projected as the green leaf area (GLA), was investigated by non-destructive RGB imaging-based phenotyping. Dynamics of carbohydrates, hexose phosphates, organic acids, proteins, and amino acids were assessed in leaf and crown tissues. Results revealed that exposure to higher low-temperature induced higher accumulation of shoot biomass and had a negative impact on FT of winter wheat. Prolonged higher low-temperature negatively affected the accumulation of soluble carbohydrates, protein content and amino acids, and had a positive effect on starch accumulation in leaf and crown tissues after CA, in comparison with the constant low-temperature treatment. DEA resulted in significantly reduced FT. Lower concentrations of glucose-6-phosphate, sucrose and proline, as well as higher concentrations of starch in leaves and crowns were found after DEA. The majority of the genotypes regained FT after REA; higher concentrations of glucose and malate in leaves, and sucrose in crown tissue were observed, whereas starch accumulation was decreased in both tissues. Negative correlations were determined between FT and starch concentration in leaves and crowns, while proline and proteins, accumulated in crowns, showed positive correlations with FT. This study broadens the knowledge regarding the effect of different low-temperature regimes on the dynamics of metabolite accumulation in winter wheat throughout CA, DEA, and REA, and its relationship to biomass accumulation and FT.

Grain Yield Performance and Quality Characteristics of Waxy and Non-Waxy Winter Wheat Cultivars under High and Low-Input Farming Systems.

Waxy starch with a modified amylose-to-amylopectin ratio is desired for a range of applications in food and non-food industries; however, yield performance and grain quality characteristics of waxy wheat cultivars are usually inferior in comparison to advanced non-waxy cultivars. In this study, we compared waxy ('Eldija', 'Sarta') and non-waxy ('Skagen', 'Suleva DS') winter wheat cultivars grown under high and low-input farming systems over two cropping seasons by evaluating their yield and grain quality, including flour, dough, and starch physicochemical properties. The yield of waxy cv. 'Sarta' was significantly lower compared to the non-waxy cultivars across all trials; however, waxy cv. 'Eldija' had a similar yield as non-waxy cultivars (except under high-input conditions cv. 'Skagen'). Moreover, no significant differences were observed between protein and gluten content of waxy and non-waxy cultivars. Low amylose content typical for waxy wheat cultivars highly correlated (r ≥ 0.8) with lower falling number, flour yield and sedimentation values, lower nitrogen % used for grain, higher flour water absorption and flour particle size index. In general, properties dependent on starch structure demonstrated consistent and significant differences between both starch types. The prevailing heat waves during the grain filling period decreased grain test weight but increased protein and gluten content and caused gluten to be weaker. Dough development time at these conditions became longer, dough softening lowered and starch content decreased, but A-starch, starch peak and final viscosity values increased. Low-input farming had a negative effect on grain yield, grain nitrogen uptake and grain test weight but increased phosphorus content in grain. The unique dough mixing properties of waxy cultivar 'Eldija' suggest that it could be used in mixtures along with non-waxy wheat for dough quality improvement.

Fungicide sensitivity levels in the Lithuanian Zymoseptoria tritici population in 2021.

Zymoseptoria tritici causes the disease known as septoria leaf blotch in winter wheat and is a major factor in yield loss worldwide. Farmers are inclined to use fungicides to protect their crops; however, the efficacy of these measures is rapidly decreasing due to the natural mechanisms of mutation emergence in pathogen populations. Increasing fungicide resistance is being recorded worldwide, therefore, screening of the current situation in Lithuania is essential to determine the subsequent steps of crop protection strategies. In this study, in vitro fungicide sensitivity tests, mutation detection, and field experiments were carried out. The mean EC50 values for prothioconazole-desthio and mefentrifluconazole were 0.14 and 0.28 mg/l, respectively. Increased frequency of the mutation S524T, linked to DMIs resistance, was observed. Results revealed that the dominant point mutation in the gene CYP51 was I381V, and the most frequent CYP51 haplotype was D13 (V136C, I381V, Y461H, S524T). The mutation G143A, linked to QoI resistance, was detected in ¾ of the population. Mutations conferring resistance to SDHIs were not detected in single pycnidium isolates. Two-year field experiments likewise showed no decline in field efficacy of SDHI fungicide in Lithuania. Moreover, the baseline sensitivity of the Lithuanian Z. tritici population to QiI fungicide fenpicoxamid was established. The findings of this study provide an update on the current status of fungicide resistance in the Lithuanian Z. tritici population.

GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage.

Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.

Proximal Phenotyping and Machine Learning Methods to Identify Septoria Tritici Blotch Disease Symptoms in Wheat.

Phenotyping with proximal sensors allow high-precision measurements of plant traits both in the controlled conditions and in the field. In this work, using machine learning, an integrated analysis was done from the data obtained from spectroradiometer, infrared thermometer, and chlorophyll fluorescence measurements to identify most predictive proxy measurements for studying Septoria tritici blotch (STB) disease of wheat. The random forest (RF) models for chlorosis and necrosis identified photosystem II quantum yield (QY) and vegetative indices (VIs) associated with the biochemical composition of leaves as the top predictive variables for identifying disease symptoms. The RF model for chlorosis was validated with a validation set (R2: 0.80) and in an independent test set (R2: 0.55). Based on the results, it can be concluded that the proxy measurements for photosystem II, chlorophyll content, carotenoid, and anthocyanin levels and leaf surface temperature can be successfully used to detect STB. Further validation of these results in the field will enable application of these predictive variables for detection of STB in the field.

Affordable Imaging Lab for Noninvasive Analysis of Biomass and Early Vigour in Cereal Crops.

Plant phenotyping by imaging allows automated analysis of plants for various morphological and physiological traits. In this work, we developed a low-cost RGB imaging phenotyping lab (LCP lab) for low-throughput imaging and analysis using affordable imaging equipment and freely available software. LCP lab comprising RGB imaging and analysis pipeline is set up and demonstrated with early vigour analysis in wheat. Using this lab, a few hundred pots can be photographed in a day and the pots are tracked with QR codes. The software pipeline for both imaging and analysis is built from freely available software. The LCP lab was evaluated for early vigour analysis of five wheat cultivars. A high coefficient of determination (R2 0.94) was obtained between the dry weight and the projected leaf area of 20-day-old wheat plants and R2 of 0.9 for the relative growth rate between 10 and 20 days of plant growth. Detailed description for setting up such a lab is provided together with custom scripts built for imaging and analysis. The LCP lab is an affordable alternative for analysis of cereal crops when access to a high-throughput phenotyping facility is unavailable or when the experiments require growing plants in highly controlled climate chambers. The protocols described in this work are useful for building affordable imaging system for small-scale research projects and for education.

A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region.

The Baltic Sea is one of the largest brackish water bodies in the world. Eutrophication is a major concern in the Baltic Sea due to the leakage of nutrients to the sea with agriculture being the primary source. Wheat (Triticum aestivum L.) is the most widely grown crop in the countries surrounding the Baltic Sea and thus promoting sustainable agriculture practices for wheat cultivation will have a major impact on reducing pollution in the Baltic Sea. This approach requires identifying and addressing key challenges for sustainable wheat production in the region. Implementing new technologies for climate-friendly breeding and digital farming across all surrounding countries should promote sustainable intensification of agriculture in the region. In this review, we highlight major challenges for wheat cultivation in the Baltic Sea region and discuss various solutions integrating transnational collaboration for pre-breeding and technology sharing to accelerate development of low input wheat cultivars with improved host plant resistance to pathogen and enhanced adaptability to the changing climate.