Consensus genomic regions for grain quality traits in wheat revealed by Meta-QTL analysis and in silico transcriptome integration.

Grain quality traits are the key factors that determine the economic value of wheat and are largely influenced by genetics and the environment. In this study, using a meta-analysis of quantitative trait loci (QTLs) and a comprehensive in silico transcriptome assessment, we identified key genomic regions and putative candidate genes for the grain quality traits protein content, gluten content, and test weight. A total of 508 original QTLs were collected from 41 articles on QTL mapping for the three quality traits in wheat published from 2003 to 2021.

Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment.

Background: Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement.

Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat.

Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades.

Identification of quantitative trait loci (QTL) and meta-QTL analysis for kernel size-related traits in wheat (Triticum aestivum L.).

Background: Kernel size-related traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR) and kernel thickness (KT), are critical determinants for wheat kernel weight and yield and highly governed by a type of quantitative genetic basis. Genome-wide identification of major and stable quantitative trait loci (QTLs) and functional genes are urgently required for genetic improvement in wheat kernel yield. A hexaploid wheat population consisting of 120 recombinant inbred lines was developed to identify QTLs for kernel size-related traits under different water environments.

Sensitivity and Specificity for the Detection of Clinical Mastitis by Automatic Milking Systems in Bavarian Dairy Herds.

In automatic milking systems (AMSs), the detection of clinical mastitis (CM) and the subsequent separation of abnormal milk should be reliably performed by commercial AMSs. Therefore, the objectives of this cross-sectional study were (1) to determine the sensitivity (SN) and specificity (SP) of CM detection of AMS by the four most common manufacturers in Bavarian dairy farms, and (2) to identify routinely collected cow data (AMS and monthly test day data of the regional Dairy Herd Improvement Association (DHIA)) that could improve the SN and SP of clinical mastitis detection. Bavarian dairy farms with AMS from the manufacturers DeLaval, GEA Farm Technologies, Lely, and Lemmer-Fullwood were recruited with the aim of sampling at least 40 cows with clinical mastitis per AMS manufacturer in addition to clinically healthy ones.

Assessing various environmental descriptors with respect to genotype x environment interaction for milk production traits in Bavarian Fleckvieh cattle.

Genotype x environment (GxE) interaction for production traits in Fleckvieh cattle was assessed by means of various environmental descriptors (EDs). It was also of particular interest to search for EDs useful for studying differing robustness or resilience of individuals which implies reasonable GxE interaction. The set of studied EDs included farm/herd environment (e.

Developing a predictive model for beta-hydroxybutyrate and non-esterified fatty acids using milk fourier-transform infrared spectroscopy in dairy cows.

Negative energy balance following parturition predisposes dairy cattle to numerous metabolic disorders. Current diagnostics are limited by their labor requirements and inability to measure multiple metabolic markers simultaneously. Fourier-transform Infrared spectroscopy (FTIR) data, measured from milk samples, could improve the detection of metabolic disorders using routine milk samples from dairy farms.

Species richness is more important for ecosystem functioning than species turnover along an elevational gradient.

Many experiments have shown that biodiversity enhances ecosystem functioning. However, we have little understanding of how environmental heterogeneity shapes the effect of diversity on ecosystem functioning and to what extent this diversity effect is mediated by variation in species richness or species turnover. This knowledge is crucial to scaling up the results of experiments from local to regional scales.

Engineering Climate-Change-Resilient Crops: New Tools and Approaches.

Environmental adversities, particularly drought and nutrient limitation, are among the major causes of crop losses worldwide. Due to the rapid increase of the world's population, there is an urgent need to combine knowledge of plant science with innovative applications in agriculture to protect plant growth and thus enhance crop yield. In recent decades, engineering strategies have been successfully developed with the aim to improve growth and stress tolerance in plants.

Suppression of an Invasive Native Plant Species by Designed Grassland Communities.

Grassland biodiversity is declining due to climatic change, land-use intensification, and establishment of invasive plant species. Excluding or suppressing invasive species is a challenge for grassland management. An example is , an invasive native plant in wet grasslands of Central Europe, that is causing problems to farmers by being poisonous, overabundant, and fast spreading.

Genotype-by-environment interactions at the trait level and total merit index level for milk production and functional traits in Brown Swiss cattle.

The production environments of the German-Austrian Brown Swiss population show a wide range due to differences in topography, landscapes, local climates, and different farm management systems. Extensive production systems such as organic farming have become increasingly popular in recent decades because of interest in sustainability and consumer preferences. Compared with conventional farmers, organic farmers put more weight on fitness traits.

Evaluation of the net energy for lactation system and estimation of the energy requirements of dairy cows based on a comprehensive analysis of feeding trials.

Respiration experiments with high-yielding dairy cows in Northern Ireland have shown higher energy maintenance requirements than those used in the requirements standards of, e.g. France, UK, USA and Germany.

Identification of , a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat.

Wheat ( L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of is a powerful method for hybrid seed production.

Novel sampling procedure to characterize bovine subclinical endometritis by uterine secretions and tissue.

Subclinical endometritis (SE) in cattle is defined as clinically unapparent inflammation of the endometrium. It is reported to impair fertility in affected cows and causes economic loss within the dairy industry. A gold standard for diagnosis of SE has not been set.

Phasing quality assessment in a brown layer population through family- and population-based software.

Background: Haplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc. In addition, haplotype structure is used to assess genetic diversity and expected accuracy in genomic selection programs. Nevertheless, the quality and efficiency of phasing has rarely been a subject of thorough study but was assessed mainly as a by-product in imputation quality studies.

A Simple Test Identifies Selection on Complex Traits.

Important traits in agricultural, natural, and human populations are increasingly being shown to be under the control of many genes that individually contribute only a small proportion of genetic variation. However, the majority of modern tools in quantitative and population genetics, including genome-wide association studies and selection-mapping protocols, are designed to identify individual genes with large effects. We have developed an approach to identify traits that have been under selection and are controlled by large numbers of loci.

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals.

Stature is affected by many polymorphisms of small effect in humans . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs.

Long-Term Impact of Optimum Contribution Selection Strategies on Local Livestock Breeds with Historical Introgression Using the Example of German Angler Cattle.

The long-term performance of different selection strategies was evaluated via simulation using the example of a local cattle breed, German Angler cattle. Different optimum contribution selection (OCS) approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution (MC) were estimated from genomic data.

Systematic review of the concentrations of oligosaccharides in human milk.

Context: Oligosaccharides are the third largest solid component in human milk. These diverse compounds are thought to have numerous beneficial functions in infants, including protection against infectious diseases. The structures of more than 100 oligosaccharides in human milk have been elucidated so far.

Accuracy of genomic breeding values revisited: Assessment of two established approaches and a novel one to determine the accuracy in two-step genomic prediction.

Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality.

Whole-genome sequence-based genomic prediction in laying chickens with different genomic relationship matrices to account for genetic architecture.

Background: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs).

Methods: A total of 892 chickens from a commercial brown layer line were genotyped with 336 K segregating SNPs (array data) that included 157 K genic SNPs (i.

Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE).

Background: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far.

Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP.

Reintroduction of rare arable plants by seed transfer. What are the optimal sowing rates?

During the past decades, agro-biodiversity has markedly declined and some species are close to extinction in large parts of Europe. Reintroduction of rare arable plant species in suitable habitats could counteract this negative trend. The study investigates optimal sowing rates of three endangered species (Legousia speculum-veneris (L.

Fighting fish parasites with photodynamically active chlorophyllin.

Water-soluble chlorophyll (chlorophyllin) was used in a phototoxic reaction against a number of fish ectoparasites such as Ichtyobodo, Dactylogyrus, Trichodina, and Argulus. Chlorophyllin is applied to the water at concentrations of several micrograms per milliliter for a predefined incubation time, and afterwards, the parasites are exposed to simulated solar radiation. Application in the dark caused only little damage to the parasites; likewise, light exposure without the addition of the photosensitizer was ineffective.

Epistasis and covariance: how gene interaction translates into genomic relationship.

Models based on additive marker effects and on epistatic interactions can be translated into genomic relationship models. This equivalence allows to perform predictions based on complex gene interaction models and reduces computational effort significantly. In the theory of genome-assisted prediction, the equivalence of a linear model based on independent and identically normally distributed marker effects and a model based on multivariate Gaussian distributed breeding values with genomic relationship as covariance matrix is well known.