A5015074074- Wheat and Barley Genetics and Pathology
- Turfgrass Adaptation and Management
- Plant and fungal interactions
- Genetic Mapping and Diversity in Plants and Animals
- Agriculture, Soil, Plant Science
- Plant Disease Resistance and Genetics
- Genetic and phenotypic traits in livestock
- Bioenergy crop production and management
- Plant Stress Responses and Tolerance
- Plant nutrient uptake and metabolism
- Plant Reproductive Biology
- Genetics and Plant Breeding
- Legume Nitrogen Fixing Symbiosis
- Plant Taxonomy and Phylogenetics
- Botanical Research and Chemistry
- Plant pathogens and resistance mechanisms
- Plant Pathogens and Resistance
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Plant Gene Expression Analysis
- Ruminant Nutrition and Digestive Physiology
- Plant Pathogens and Fungal Diseases
- Horticultural and Viticultural Research
- Plant-Microbe Interactions and Immunity
- Yeasts and Rust Fungi Studies
Aarhus University
2016-2025
Slagelse Hospital
2018-2021
Iowa State University
2012
Institute of Bioinformatics and Systems Biology
2012
Helmholtz Zentrum München
2012
Aberystwyth University
2010
Institute of Biological, Environmental and Rural Sciences
2010
University of Copenhagen
2002
Genomic selection (GS) is becoming increasingly applicable to crops as the genotyping costs continue decrease, which makes it an attractive alternative traditional selective breeding based on observed phenotypes. With genome-wide molecular markers, predictions from genotypes can be made in absence of direct phenotyping. The reliability depends strongly number individuals used for training predictive algorithms, particularly a highly genetically diverse organism such potatoes; however,...
Summary Here we report the draft genome sequence of perennial ryegrass ( Lolium perenne ), an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It classified along with wheat, barley, oats Brachypodium distachyon Pooideae sub‐family family (Poaceae). Transcriptome data was used to identify 28 455 gene models, utilized macro‐co‐linearity between synteny within family, establish a synteny‐based linear order. The gametophytic...
The merging of distinct genomes, allopolyploidization, is a widespread phenomenon in plants. It generates adaptive potential through increased genetic diversity, but examples demonstrating its exploitation remain scarce. White clover (Trifolium repens) ubiquitous temperate allotetraploid forage crop derived from two European diploid progenitors confined to extreme coastal or alpine habitats. We sequenced and assembled the genomes transcriptomes this species complex gain insight into genesis...
Genotyping-by-Sequencing (GBS) is an excellent tool for characterising genetic variation between plant genomes. To date, its use has been reported only genotyping of single individuals. However, there are many applications where resolving allele frequencies within populations on a genome-wide scale would be very powerful, examples include the breeding outbreeding species, varietal protection in monitoring changes population frequencies. This motivated us to test potential GBS evaluate...
Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. uses genome-wide molecular markers to predict performance of individuals allows selections the absence direct phenotyping. It regarded as useful tool accelerate genetic gain programs, becoming increasingly viable crops genotyping costs continue fall. In this study, we have generated potato facilitate varietal...
Abstract Whole-genome sequences established for model and major crop species constitute a key resource advanced genomic research. For outbreeding forage turf grass like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present of the perennial ryegrass perenne) genome on basis conserved synteny barley (Hordeum vulgare) Brachypodium (Brachypodium distachyon) as well rice (Oryza sativa) sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map served...
Genomic selection (GS) has become a commonly used technology in animal breeding. In crops, it is expected to significantly improve the genetic gains per unit of time. So far, its implementation plant breeding been mainly investigated species farmed as homogeneous varieties. Concerning crops family pools, only few theoretical studies are currently available. Here, we test opportunity implement GS perennial ryegrass, using real data from forage program. Heading date was chosen model trait, due...
The grass family (Poaceae), the fourth largest of flowering plants, encompasses most economically important cereal, forage, and energy crops, exhibits a unique gametophytic self-incompatibility (SI) mechanism that is controlled by at least two multiallelic independent loci, S Z. Despite intense research efforts over last six decades, genes underlying Z remain uncharacterized. Here, we report fine-mapping approach to identify male component S-locus in perennial ryegrass (Lolium perenne L.)...
Genomic selection is focused on prediction of breeding values candidates by means high density markers. It relies the assumption that all quantitative trait loci (QTLs) tend to be in strong linkage disequilibrium (LD) with at least one marker. In this context, we present theoretical results regarding accuracy genomic selection, i.e., correlation between predicted and true values. Typically, for individuals (so-called test individuals), are markers, using marker effects estimated fitting a...
Abstract Background The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well for evolutionary comparative genomics. improvement long-read sequencing technologies the advent optical mapping chromosome conformation capture last few years, significantly promoted development model plants crop species. In grasses, recently became available cultivated wild species Triticeae subfamily. Development state-of-the-art genomic...
Abstract Background Grasses are adapted to a wide range of climatic conditions. Species the subfamily Pooideae, which includes wheat, barley and important forage grasses, have evolved extreme frost tolerance. A class ice binding proteins that inhibit re-crystallisation, specific Pooideae lineage, been identified in perennial ryegrass these thought from leucine-rich repeat phytosulfokine receptor kinase ( LRR-PSR )-like ancestor gene. Even though re-crystallisation inhibition function has...
Single nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in genome and ability be used highly multiplexed genotyping assays. Although needed high numbers for genome-wide profiles genomics-assisted breeding, a surprisingly low number validated SNPs currently available perennial ryegrass. A ryegrass unigene set representing 9,399 genes was as reference assembly 802,156 quality reads generated by 454 transcriptome sequencing silico...
Ryegrass single plants, bi-parental family pools, and multi-parental pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage leads a higher proportion of missing data, reduction in accuracy when identifying allele-frequency each locus. As consequence latter, genomic relationship matrices (GRMs) will biased. This bias GRMs affects variance estimates...
Lupins (Lupinus spp.) are nitrogen-fixing legumes that accumulate toxic alkaloids in their protein-rich beans. These anti-nutritional compounds belong to the family of quinolizidine (QAs), which interest pharmaceutical and chemical industries. To unleash potential lupins as protein crops sources QAs, a thorough understanding QA pathway is needed. However, only first enzyme pathway, lysine decarboxylase (LDC), known. Here, we report transcriptome high-QA variety narrow-leafed lupin (L....
Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone intergenomic DNA transfers, leading the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies in their infancy some key aspects of evolution still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning silico enrichment mitochondrial-like long reads...
Abstract Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance their xeric environments. They employ various strategies overcome environmental constraints, such as crassulacean acid metabolism, wax depositions, and protective leaf morphology. Genomic resources Agave species have received little attention irrespective cultural, economic ecological importance, which so far prevented the understanding molecular bases underlying...
Abstract Lotus japonicus is a herbaceous perennial legume that has been used extensively as genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim to improve L. reference genome sequence, which so far based on Sanger and Illumina sequencing reads from accession MG-20 contained large fraction unanchored contigs. Here, we use long PacBio Gifu combined with Hi-C data new high-density genetic maps generate high-quality chromosome-scale...
Abstract Background Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium ryegrass lacking, which essential the efficiency of association analyses. Results 11 expressed disease resistance candidate (R) genes including 6 binding site leucine rich repeat (NBS-LRR) like 5 non-NBS-LRR were analyzed diversity. For each about 1 kb genomic fragments isolated from 20 heterozygous genotypes The number haplotypes...
Simple sequence repeat (SSR) markers are highly informative and widely used for genetic breeding studies in several plant species. They cultivar identification, variety protection, as anchor mapping, marker-assisted breeding. Currently, a limited number of SSR publicly available perennial ryegrass (Lolium perenne). We report on the exploitation comprehensive EST collection L. perenne identification. The objectives this study were 1) to analyse frequency, type, distribution motifs ESTs...
The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role the photoperiodic induction of flowering response. genomic phenotypic variations associated with perennial ryegrass (Lolium perenne) ortholog FT, designated LpFT3, was assessed a diverse collection nine European germplasm populations, which together constituted association panel 864 plants. Sequencing genotyping series...
Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection map-based cloning. In the case of key grassland species Lolium spp., numerous populations have been developed characterised various traits. Although some genetic maps these aligned with each other using publicly available DNA markers, number common among is still low, limiting ability to compare candidate gene QTL locations across germplasm. A set 204 expressed sequence tag (EST)-derived simple repeat...
Background Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome of such as perennial challenging. Creating reference from homozygous genotype circumvent the challenge heterozygosity. The goals this study were to perform RNA-sequencing on multiple tissues inbred develop transcriptome. This was complemented with SNP calling. Result De created 185,833 transcripts...
We propose a method in which GBS data can be conveniently analyzed without calling genotypes. F2 families are frequently used breeding of outcrossing species, for instance to obtain trait measurements on plots. perform association studies by obtaining matching "family genotype" from sequencing pooled sample the family, and directly use allele frequencies computed sequence read-counts mapping. show that, under additivity assumptions, there is linear relationship between family phenotype...
Perennial ryegrass (Lolium perenne L.) produces high levels of fructans as a mixture oligomers with different degrees polymerization (DP). The present study describes the analysis compositional changes in full spectrum fructan oligomers, distribution between above ground biomass (top) and roots, transcription candidate genes involved metabolism during cold acclimation perennial variety 'Veyo' ecotype 'Falster' from distinct geographical origins. We observed composition induction low-DP...