Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program.

Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem.

Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding.

The integration of target capture systems with next-generation sequencing has emerged as an efficient tool for exploring specific genetic regions with a high resolution and facilitating the rapid discovery of novel alleles. Despite these advancements, the application of targeted sequencing methodologies, such as the myBaits technology, in polyploid oat species remains relatively unexplored. In this study, we utilized the myBaits target capture method offered by Daicel Arbor Biosciences to detect variants and assess their reliability for variant detection in oat genomics and breeding.

Scald resistance in hybrid rye (): genomic prediction and GWAS.

Rye (.) is an important cereal crop used for food, beverages, and feed, especially in North-Eastern Europe. While rye is generally more tolerant to biotic and abiotic stresses than other cereals, it still can be infected by several diseases, including scald caused by .

Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet.

Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses.

Metabolomic-genomic prediction can improve prediction accuracy of breeding values for malting quality traits in barley.

Background: Metabolomics measures an intermediate stage between genotype and phenotype, and may therefore be useful for breeding. Our objectives were to investigate genetic parameters and accuracies of predicted breeding values for malting quality (MQ) traits when integrating both genomic and metabolomic information. In total, 2430 plots of 562 malting spring barley lines from three years and two locations were included.

Genomic prediction for grain yield and micro-environmental sensitivity in winter wheat.

Individuals within a common environment experience variations due to unique and non-identifiable micro-environmental factors. Genetic sensitivity to micro-environmental variation (i.e.

Integrating a growth degree-days based reaction norm methodology and multi-trait modeling for genomic prediction in wheat.

Multi-trait and multi-environment analyses can improve genomic prediction by exploiting between-trait correlations and genotype-by-environment interactions. In the context of reaction norm models, genotype-by-environment interactions can be described as functions of high-dimensional sets of markers and environmental covariates. However, comprehensive multi-trait reaction norm models accounting for marker × environmental covariates interactions are lacking.

Metabolomic spectra for phenotypic prediction of malting quality in spring barley.

We investigated prediction of malting quality (MQ) phenotypes in different locations using metabolomic spectra, and compared the prediction ability of different models, and training population (TP) sizes. Data of five MQ traits was measured on 2667 individual plots of 564 malting spring barley lines from three years and two locations. A total of 24,018 metabolomic features (MFs) were measured on each wort sample.

Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics.

The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of f. sp.

Discovery of a Novel Leaf Rust () Resistance Gene in Rye ( L.) Using Association Genomics.

Leaf rust constitutes one of the most important foliar diseases in rye ( L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019.

Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis.

Including additive and additive-by-additive epistasis in a NOIA parametrization did not yield orthogonal partitioning of genetic variances, nevertheless, it improved predictive ability in a leave-one-out cross-validation for wheat grain yield. Additive-by-additive epistasis is the principal non-additive genetic effect in inbred wheat lines and is potentially useful for developing cultivars based on total genetic merit; nevertheless, its practical benefits have been highly debated. In this article, we aimed to (i) evaluate the performance of models including additive and additive-by-additive epistatic effects for variance components (VC) estimation of grain yield in a wheat-breeding population, and (ii) to investigate whether including additive-by-additive epistasis in genomic prediction enhance wheat grain yield predictive ability (PA).

Genomic Scan of Male Fertility Restoration Genes in a 'Gülzow' Type Hybrid Breeding System of Rye ( L.).

Efficient and stable restoration of male fertility (Rf) is a prerequisite for large-scale hybrid seed production but remains an inherent issue in the predominant fertility control system of rye ( L.). The 'Gülzow' (G)-type cytoplasmic male sterility (CMS) system in hybrid rye breeding exhibits a superior Rf.

Multi-Parental Populations Suitable for Identifying Sources of Resistance to Powdery Mildew in Winter Wheat.

Wheat ( L.) is one of the world's staple food crops and one of the most devastating foliar diseases attacking wheat is powdery mildew (PM). In Denmark only a few specific fungicides are available for controlling PM and the use of resistant cultivars is often recommended.

Prediction of complex phenotypes using the Drosophila melanogaster metabolome.

Understanding the genotype-phenotype map and how variation at different levels of biological organization is associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at DNA level and on intermediate endophenotypes, such as RNA, proteins and metabolites. This can facilitate our understanding of the link between genotypes and molecular and functional organismal phenotypes.

A Comparative Transcriptome Analysis, Conserved Regulatory Elements and Associated Transcription Factors Related to Accumulation of Fusariotoxins in Grain of Rye ( L.) Hybrids.

Detoxification of fusariotoxin is a type V Fusarium head blight (FHB) resistance and is considered a component of type II resistance, which is related to the spread of infection within spikes. Understanding this type of resistance is vital for FHB resistance, but to date, nothing is known about candidate genes that confer this resistance in rye due to scarce genomic resources. In this study, we generated a transcriptomic resource.

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.).

Rye (Secale cereale L.) responds strongly to changes in heterozygosity with hybrids portraying strong heterosis effect on all developmental and yielding characteristics. In order to achieve the highest potential heterosis effect parental lines must originate from genetically distinct gene pools.

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea).

Rye is used as food, feed, and for bioenergy production and remain an essential grain crop for cool temperate zones in marginal soils. Ergot is known to cause severe problems in cross-pollinated rye by contamination of harvested grains. The molecular response of the underlying mechanisms of this disease is still poorly understood due to the complex infection pattern.

Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds.

Whole-genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace [LL], and Yorkshire [YY]) was performed. Twenty-six million single-nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a high functional impact such as gain or loss of stop codon.

Genetic Signatures of Drug Response Variability in .

Knowledge of the genetic basis underlying variation in response to environmental exposures or treatments is important in many research areas. For example, knowing the set of causal genetic variants for drug responses could revolutionize personalized medicine. We used to investigate the genetic signature underlying behavioral variability in response to methylphenidate (MPH), a drug used in the treatment of attention-deficit/hyperactivity disorder.

Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle1.

In recent years, metabolomics has been used to clarify the biology underlying biological samples. In the field of animal breeding, investigating the magnitude of genetic control on the metabolomic profiles of animals and their relationships with quantitative traits adds valuable information to animal improvement schemes. In this study, we analyzed metabolomic features (MFs) extracted from the metabolomic profiles of 843 male Holstein calves.

Functional Validation of Candidate Genes Detected by Genomic Feature Models.

Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait.

Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster.

Background: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations.

Results: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods.

Mild heat treatments induce long-term changes in metabolites associated with energy metabolism in Drosophila melanogaster.

Heat-induced hormesis, the beneficial effect of mild heat-induced stress, increases the average lifespan of many organisms. Yet little is known about the mechanisms underlying this effect. We used nuclear magnetic resonance spectroscopy to investigate the long-term effects of repeated mild heat treatments on the metabolome of male Drosophila melanogaster.

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster.

Predicting individual quantitative trait phenotypes from high-resolution genomic polymorphism data is important for personalized medicine in humans, plant and animal breeding, and adaptive evolution. However, this is difficult for populations of unrelated individuals when the number of causal variants is low relative to the total number of polymorphisms and causal variants individually have small effects on the traits. We hypothesized that mapping molecular polymorphisms to genomic features such as genes and their gene ontology categories could increase the accuracy of genomic prediction models.