Structural variation in the pangenome of wild and domesticated barley.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes.

Bacterial N-Acyl Homoserine Lactone Priming Enhances Leaf-Rust Resistance in Winter Wheat and Some Genomic Regions Are Associated with Priming Efficiency.

Leaf rust () is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated adaptability of pathogen populations hamper achieving durable resistance in wheat.

PEG treatment is unsuitable to study root related traits as it alters root anatomy in barley (Hordeum vulgare L.).

Background: The frequency and severity of abiotic stress events, especially drought, are increasing due to climate change. The plant root is the most important organ for water uptake and the first to be affected by water limitation. It is therefore becoming increasingly important to include root traits in studies on drought stress tolerance.

Origin and evolution of the bread wheat D genome.

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat.

Phenomic Selection for Hybrid Rapeseed Breeding.

Phenomic selection is a recent approach suggested as a low-cost, high-throughput alternative to genomic selection. Instead of using genetic markers, it employs spectral data to predict complex traits using equivalent statistical models. Phenomic selection has been shown to outperform genomic selection when using spectral data that was obtained within the same generation as the traits that were predicted.

Genomic prediction in : evaluating the benefit of imputed whole-genome sequencing data.

Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets.

Phenotyping and Exploitation of Kompetitive Allele-Specific PCR Assays for Genes Underpinning Leaf Rust Resistance in New Spring Wheat Mutant Lines.

Leaf rust ( Eriks) is a wheat disease causing substantial yield losses in wheat production globally. The identification of genetic resources with permanently effective resistance genes and the generation of mutant lines showing increased levels of resistance allow the efficient incorporation of these target genes into germplasm pools by marker-assisted breeding. In this study, new mutant (M generation) lines generated from the rust-resistant variety Kazakhstanskaya-19 were developed using gamma-induced mutagenesis through 300-, 350-, and 400-Gy doses.

Wild grapes of Armenia: unexplored source of genetic diversity and disease resistance.

The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed.

Risk assessment requires several bee species to address species-specific sensitivity to insecticides at field-realistic concentrations.

In the European registration process, pesticides are currently mainly tested on the honey bee. Since sensitivity data for other bee species are lacking for the majority of xenobiotics, it is unclear if and to which extent this model species can adequately serve as surrogate for all wild bees. Here, we investigated the effects of field-realistic contact exposure to a pyrethroid insecticide, containing lambda-cyhalothrin, on seven bee species (Andrena vaga, Bombus terrestris, Colletes cunicularius, Osmia bicornis, Osmia cornuta, Megachile rotundata, Apis mellifera) with different life history characteristics in a series of laboratory trials over two years.

From Petri Dish to Field: Plant Tissue Culture and Genetic Engineering of Oats for Improved Agricultural Outcomes.

Oats () hold immense economic and nutritional value as a versatile crop. They have long been recognized as an exceptional choice for human consumption and animal feed. Oats' unique components, including proteins, starches, and β-glucans, have led to its widespread use in various food products such as bread, noodles, flakes, and milk.

Stage-specific genotype-by-environment interactions determine yield components in wheat.

In cereal crops, environmental fluctuations affect different physiological processes during various developmental phases associated with the formation of yield components. Because these effects are coupled with cultivar-specific phenology, studies investigating environmental responses in different cultivars can give contradictory results regarding key phases impacting yield performance. To dissect how genotype-by-environment interactions affect grain yield in winter wheat, we estimated the sensitivities of yield components to variation in global radiation, temperature and precipitation in 220 cultivars across 81 time-windows ranging from double ridge to seed desiccation.

A Reliable and Simple Method for the Production of Viable Pycnidiospores of the Pine Pathogen and a Spore-Based Infection Assay on Scots Pine.

is a globally distributed opportunistic fungal pathogen of conifers that causes severe production losses in forestry. The fungus frequently colonizes pine trees as an endophyte without causing visible symptoms but can become pathogenic when the host plant is weakened by stress, such as drought or heat. Forest damage might therefore further increase due to the effects of climate change.

A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in L.

Root chicory ( L. var. ) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic.

Genetic mapping of the powdery mildew resistance gene Pm7 on oat chromosome 5D.

Three independent experiments with different genetic backgrounds mapped the resistance gene Pm7 in the oat genome to the distal part of the long arm of chromosome 5D. Resistance of oat to Blumeria graminis DC. f.

PCR Allele Competitive Extension (PACE).

PCR allele competitive extension (PACE™) is a marker system to analyze single nucleotide polymorphisms (SNPs). As strongly related technologies like kompetitive allele-specific PCR (KASP™) or Amplifluor, PACE is based on a polymerase chain reaction (PCR) with two competing allele-specific primers and an endpoint fluorescent measurement. The system requires sequence information surrounding the SNP of interest and a qPCR machine or a fluorescent plate reader.

Novel resistance to the Bymovirus BaMMV established by targeted mutagenesis of the PDIL5-1 susceptibility gene in barley.

The Potyviridae are the largest family of plant-pathogenic viruses. Members of this family are the soil-borne bymoviruses barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), which, upon infection of young winter barley seedlings in autumn, can cause yield losses as high as 50%. Resistance breeding plays a major role in coping with these pathogens.

Genome editing around the globe: An update on policies and perceptions.

A decade ago, the CRISPR/Cas system has been adapted for genome editing. Since then, hundreds of organisms have been altered using genome editing and discussions were raised on the regulatory status of genome edited organisms esp. crops.

High-Resolution Mapping of Resistance Gene .

(BaYMV) and (BaMMV), which are transmitted by the soil-borne plasmodiophorid , cause high yield losses in barley. In previous studies, the recessive BaMMV resistance gene , derived from the Japanese landrace Chikurin Ibaraki 1, was mapped on chromosome 6HS of . In this study, 423 F segmental recombinant inbred lines (RILs) were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri (139 RILs) and Uschi (284 RILs).

Sanitary measures considerably improve the management of resistant Norway rats on livestock farms.

Background: Norway rats (Rattus norvegicus) need to be controlled to prevent transmission of pathogens and damages to stored products and material, leading to considerable economic risks and losses. Given increasing resistance in Norway rats, the most persistent, bio-accumulative and toxic anticoagulant rodenticides are widely used for management, which presents hazards to the environment especially for non-target species. We investigated how sanitary measures improved management of Norway rats on 12 paired livestock farms in a region of Germany with a high population of resistant rats for reducing application of rodenticides.

Targeted Knockout of Eukaryotic Translation Initiation Factor 4E Confers Bymovirus Resistance in Winter Barley.

The Eukaryotic Translation Initiation Factor 4E (EIF4E) is a well-known susceptibility factor for potyvirus infections in many plant species. The barley yellow mosaic virus disease, caused by the bymoviruses (BaYMV) and (BaMMV), can lead to yield losses of up to 50% in winter barley. In autumn, the roots of young barley plants are infected by the soil-borne plasmodiophoraceous parasite L.

Heterologous Complementation of SPO11-1 and -2 Depends on the Splicing Pattern.

In the past, major findings in meiosis have been achieved, but questions towards the global understanding of meiosis remain concealed. In plants, one of these questions covers the need for two diverse meiotic active SPO11 proteins. In and other plants, both meiotic SPO11 are indispensable in a functional form for double strand break induction during meiotic prophase I.

The consensus rye microsatellite map with EST-SSRs transferred from wheat.

Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped.

How Population Structure Impacts Genomic Selection Accuracy in Cross-Validation: Implications for Practical Breeding.

Over the last two decades, the application of genomic selection has been extensively studied in various crop species, and it has become a common practice to report prediction accuracies using cross validation. However, genomic prediction accuracies obtained from random cross validation can be strongly inflated due to population or family structure, a characteristic shared by many breeding populations. An understanding of the effect of population and family structure on prediction accuracy is essential for the successful application of genomic selection in plant breeding programs.