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Abstract BackgroundIn breeding the aim is to identify and accumulate beneficial variants. However, detection of these variants may be challenging in the presence of extensive genotype x environment interactions (GxE), as variant effects will be conditional on environment.MethodsThe study assesses the performance of264diploid perennial ryegrass accessions in a multi-environment field trial. We investigate the extent of GxE, for yield (total dry matter) and persistence traits, i.e. winter kill and spring cover, under environmental conditions experienced in Nordic and Baltic regions at the limit of the species distribution. Two different approaches to modelling GxE were tested: reaction norm and envirotyping, and the models were validated under three different breeding scenarios.ResultsOur analysis documented the presence of significant GxE interaction for all traits investigated in the study. Validation showed improvements in prediction accuracy when accounting for GxE: up to 4% for yield when predicting in unobserved environments, and up to 22% and 9% for spring cover and winter kill, respectively when predicting unobserved germplasm. Genome-wide-association-studies (GWAS) were utilized to detect genetic variants with marginal effects (environment-independent effect) and conditional effects (environment-dependent effects). Results showed the presence of large-effect genetic variants with marginal effects, in addition to few QTL whose effects were adaptive under specific environmental conditions while neutral or deleterious under different environmental conditions.ConclusionThis study demonstrates the usefulness and limitations of genomic prediction models for predicting GxE in highly diverse samples, and describes the extent of GxE interactions at the limit of species distribution for perennial ryegrass. Finally, our study points toward adaptive variation, which may enhance persistence of perennial ryegrass populations in Nordic and Baltic growing conditions.

Abstract Three species of Aphanomyces, A. euteiches, A. cochlioides and A. cladogamus are devastating agricultural plant pathogens causing root rot disease on pea, sugar beet and spinach, respectively. Here we investigated the distribution of the three Aphanomyces species in parts of Sweden, Denmark and Lithuania using climate chamber soil bioassays, and tested for correlations with macronutrient levels in the soil. Aphanomyces euteiches was the most widespread pathogen found in 28% of the tested samples in Sweden and Denmark, while A. cochlioides had a more limited distribution, and was found in 22% of the samples. Aphanomyces cladogamus was only detected in Sweden and was present in 16% of the tested samples. Aphanomyces euteiches only infected pea plants, while A. cochlioides and A. cladogamus infected both sugar beet and spinach. There were significant (P < 0.001) differences in disease severity index (DSI) between regions, pathogens and for the interaction between regions and crops. Soil calcium (Ca) content ranged from 82 to 3600 mg/100 g dry soil. No species of Aphanomyces was detected in soils with Ca levels above 250 mg/100 g soil, indicating a pathogen-suppressive effect from calcium. Similar results were observed from 1350 soil samples collected from commercial pea growing fields, as DSI values on pea remained very low (below 20 on a 0–100 scale) in soil samples with confirmed presence of A. euteiches and a Ca value above 210 mg/100 g soil. High Ca levels was a significant (P < 0.05) predictor for low probability of presence of Aphanomyces spp. in soil.

Thermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.

Feruloylated arabinoxylan (AX) is a potential health-promoting fiber ingredient that can enhance nutritional properties of bread but is also known to affect dough rheology. To determine the role of feruloylation and hydrolysis of wheat bran AX on dough quality and microstructure, hydrolyzed and unhydrolyzed AX fractions with low and high ferulic acid content were produced, and their chemical composition and properties were evaluated. These fractions were then incorporated into wheat dough, and farinograph measurements, large and small deformation measurements and dough microstructure were assessed. AX was found to greatly affect both fraction properties and dough quality, and this effect was modulated by hydrolysis of AX. These results demonstrated how especially unhydrolyzed fiber fractions produced stiff doughs with poor extensibility due to weak gluten network, while hydrolyzed fractions maintained a dough quality closer to control. This suggests that hydrolysis can further improve the baking properties of feruloylated wheat bran AX. However, no clear effects from AX feruloylation on dough properties or microstructure could be detected. Based on this study, feruloylation does not appear to affect dough rheology or microstructure, and feruloylated wheat bran arabinoxylan can be used as a bakery ingredient to potentially enhance the nutritional quality of bread.

Oats, a highly nutritious cereal known for their health benefits, contain various macromolecules of significant biological value, including abundant and highly digestible proteins. Despite their importance, oat proteins have not been extensively studied. Here, we present a complete set of the expressed globulins genes, which code for the main storage protein in oats as well as their chromosomal positions. Published expressed sequence tags for globulins were used as queries in the Sang oat genome. In addition, globulin proteins were fractionated from oat flour by solvent extraction based on differential solubility with other classes of cereal proteins. The protein fractions were separated by gel electrophoresis and analyzed by tandem mass spectrometry to confirm their identity and expression in seed. In total 32 globulin gene sequences were identified on the oat genome. Out of these, the expression on RNA level could be confirmed and 27 were also detected as expressed proteins by MS. Our results provide the most extensive set of salt-soluble oat globulin sequences to date, paving the way for further understanding their implications for human nutrition. In addition, a simple methodology to fractionate oat proteins is presented.

There is a balance between DM yield and feed value when choosing types of grasses on a farm depending on the acreages of farmland and types of ruminants to be fed. Therefore, optimisation of the harvest strategy for grass silage is important for profitable dairy farming. Tall fescue has high DM yield and can replace traditional grasses, such as timothy, in Northern Europe in a changing climate as it has been shown to be more drought tolerant. As differences in climate responses previously have been related to differences in cell wall structure between grass species and, consequently, in digestibility, it is highly relevant to compare these species at similar maturity stages and to investigate if a very early harvest date will diminish potential differences between the species. This study evaluated the effects of harvest date and forage species on the concentration of hydroxycinnamic acids in silages and its relationship to feed efficiency of dairy cows. Tall fescue and timothy were harvested at very early date on May 25 or at early date on May 31 in the spring growth cycle. Forty lactating dairy cows were used in a block design. Cows received 1 of 4 treatments: (1) tall fescue harvested at very early date, (2) timothy harvested at very early date, (3) tall fescue harvested at early date, and (4) timothy harvested at early date. Diets were formulated to have the same forage-to-concentrate ratio (49:51 on DM basis). Tall fescue silages showed greater concentrations of DM, ash, and CP than timothy silages. Grasses harvested at early date showed greater concentrations of NDF, ADL, and cell wall than grasses harvested at very early date. Tall fescue silages showed greater concentration of p-coumaric acid and lower in vitro organic matter digestibility (IVOMD) compared to timothy silages. Milk production and composition were not affected by treatments but cows fed tall fescue-based diets showed lower milk protein yield and greater milk urea nitrogen than when timothy-based diets were fed. Furthermore, cows receiving timothy-based diets showed greater feed efficiency compared to cows receiving tall fescue-based diets. Thus, the lower concentration of p-coumaric acid and the higher IVOMD was associated with greater feed efficiency of cows fed timothy-based diets compared to tall fescue-based diets.

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53–0.75 and 0.36–0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.

Modern crop production is characterized by high nitrogen (N) application rates, which can influence the co-limitation of harvested yield by other nutrients. Using a multidimensional niche volume concept and scaling exponents frequently applied in plant ecological research, we report that increased N and phosphorus (P) uptake in a growing wheat crop along with enhanced grain biomass is associated with more than proportional increase of other nutrients. Furthermore, N conversion efficiency and grain yield are strongly affected by the magnesium (Mg) to P ratio in the growing crop. We analyzed a field trial in Central Sweden including nine wheat varieties grown during two years with contrasting weather, and found evidence for Mg co-limitation at lower grain yields and P co-limitation at higher yields. We argue that critical concentrations of single nutrients, which are often applied in agronomy, should be replaced by nutrient ratios. In addition, links between plant P and Mg contents and root traits were found; high root number enhanced the P:N ratio, whilst steep root angle, indicating deep roots, increased the Mg:N ratio. The results have significant implications on the management and breeding targets of agriculturally grown wheat, which is one of the most important food crops worldwide.

Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.