Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.

Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations.

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat.

PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades.

Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.

Structural variations (SVs) are larger polymorphisms (> 50 bp in length), which consist of insertions, deletions, inversions, duplications, and translocations. They can have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies, including Oxford Nanopore, allows for comprehensive SV discovery and characterization even in complex polyploid crop genomes.

Direct access to millions of mutations by whole genome sequencing of an oilseed rape mutant population.

Induced mutations are an essential source of genetic variation in plant breeding. Ethyl methanesulfonate (EMS) mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In the present study, a rapeseed M population was derived from M parent cultivar 'Express' treated with EMS.

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of Homoeologs in Hexaploid Wheat.

The gene () is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat () harbors three homoeologous loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat.

Development of Breeder-Friendly KASP Markers from Genome-Wide Association Studies Results.

Array-based SNP markers are commonly used in genome-wide association studies (GWAS) to identify genomic regions involved in important agronomical traits. However, conversion of these SNP markers into breeder-friendly kompetitive allele-specific PCR (KASP) markers for use in marker-assisted selection is often challenging. In this chapter we describe general considerations and successfully applied protocols for the conversion of Illumina array SNP markers into locus-specific KASP markers with a special emphasis and examples on how to overcome difficulties in polyploid wheat.

Perspectives for integrated insect pest protection in oilseed rape breeding.

In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again.

A toolkit to rapidly modify root systems through single plant selection.

Background: The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits.

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene in Elite .

Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry gene-mediated qualitative resistances that confer a high level of race-specific protection against , the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen's avirulence genes.

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in cv. Tosca.

Clubroot, caused by infection, is a disease of growing importance in cruciferous crops, including oilseed rape (). The affected plants exhibit prominent galling of the roots that impairs their capacity for water and nutrient uptake, which leads to growth retardation, wilting, premature ripening, or death. Due to the scarcity of effective means of protection against the pathogen, breeding of resistant varieties remains a crucial component of disease control measures.

A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape.

A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes.

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant.

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single-nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small- (30-10 000 bp) to mid-scale (10 000-30 000 bp) SV and their impact on evolution and adaptation-related traits in plants.

Chromosome-Scale Assembly of Winter Oilseed Rape .

Rapeseed (), the second most important oilseed crop globally, originated from an interspecific hybridization between and . After this genome collision, underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like , and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome.

Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum.

Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants.

Modulation of Cognitive and Emotional Control in Age-Related Mild-to-Moderate Hearing Loss.

Progressive hearing loss is a common phenomenon in healthy aging and may affect the perception of emotions expressed in speech. Elderly with mild to moderate hearing loss often rate emotional expressions as less emotional and display reduced activity in emotion-sensitive brain areas (e.g.

Genetic insights into underground responses to Fusarium graminearum infection in wheat.

The ongoing global intensification of wheat production will likely be accompanied by a rising pressure of Fusarium diseases. While utmost attention was given to Fusarium head blight (FHB) belowground plant infections of the pathogen have largely been ignored. The current knowledge about the impact of soil borne Fusarium infection on plant performance and the underlying genetic mechanisms for resistance remain very limited.

Finding invisible quantitative trait loci with missing data.

Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures.

The Influence of Negative Emotion on Cognitive and Emotional Control Remains Intact in Aging.

Healthy aging is characterized by a gradual decline in cognitive control and inhibition of interferences, while emotional control is either preserved or facilitated. Emotional control regulates the processing of emotional conflicts such as in irony in speech, and cognitive control resolves conflict between non-affective tendencies. While negative emotion can trigger control processes and speed up resolution of both cognitive and emotional conflicts, we know little about how aging affects the interaction of emotion and control.

Specific contributions of basal ganglia and cerebellum to the neural tracking of rhythm.

How specific brain networks track rhythmic sensory input over time remains a challenge in neuroimaging work. Here we show that subcortical areas, namely the basal ganglia and the cerebellum, specifically contribute to the neural tracking of rhythm. We tested patients with focal lesions in either of these areas and healthy controls by means of electroencephalography (EEG) while they listened to rhythmic sequences known to induce selective neural tracking at a frequency corresponding to the most-often perceived pulse-like beat.

Is laughter a better vocal change detector than a growl?

The capacity to predict what should happen next and to minimize any discrepancy between an expected and an actual sensory input (prediction error) is a central aspect of perception. Particularly in vocal communication, the effective prediction of an auditory input that informs the listener about the emotionality of a speaker is critical. What is currently unknown is how the perceived valence of an emotional vocalization affects the capacity to predict and detect a change in the auditory input.

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus.

Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B.

Positive emotion impedes emotional but not cognitive conflict processing.

Cognitive control enables successful goal-directed behavior by resolving a conflict between opposing action tendencies, while emotional control arises as a consequence of emotional conflict processing such as in irony. While negative emotion facilitates both cognitive and emotional conflict processing, it is unclear how emotional conflict processing is affected by positive emotion (e.g.

Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus.

Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes.