Roland Kölliker

Last Name

Kölliker

First Name

Roland

ORCID

0000-0003-1959-0402

Organisational unit

03969 - Studer, Bruno / Studer, Bruno

Show all metadata

Search Results

Publications 1 - 10 of 84

Elucidating the genetic control of bacterial wilt resistance in Italian ryegrass
Kölliker, Roland (2025)
2025 Bacterial Leaf Streak Meeting Abstracts
Xanthomonas translucens pv. graminis (Xtg) causes bacterial wilt, one of the most important forage grass diseases in temperate grasslands. Molecular genetic and genomic tools have the potential to significantly benefit resistance breeding and to enable targeted resistance management. In the past, a major QTL for bacterial wilt resistance was identified in Lolium multiflorum and Xtg was shown to rely on a non-canonical type III secretion system for plant infection. A number of candidate genes for bacterial wilt resistance were identified using a bulked segregant analysis approach. Whole genome sequencing of susceptible and resistant pools of a large biparental F2 population revealed a ~330kb region associated to bacterial wilt resistance. Comparative genomics of different X. translucens pathovars allowed to identify virulence traits characteristic for Xtg. A high number of transposases were exclusively found in Xtg 25 and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile 26 genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The candidate plant resistance genes together with the bacterial virulence factors identified provide an invaluable resource for the development of genomics assisted selection strategies. In addition, the well characterised plant genotypes and bacterial strains serve as an ideal model system to fully understand the complex L. multiflorum - Xtg interaction.
A diploid phased genome assembly of the Italian ryegrass (Lolium multiflorum Lam.) cv. Rabiosa
Copetti, Dario; Kuon, Joel‑Elias; Yates, Steven; et al. (2019)
Grassland Science in Europe ~ Improving Sown Grasslands Through Breeding and Management
Candidate genes for stem rust resistance in Italian ryegrass revealed by nested association mapping
Kiesbauer, Jenny; Grieder, Christoph; Ariza-Suarez, Daniel; et al. (2024)
German Plant Breeding Conference 2024. Abstract Book
Italian ryegrass (Lolium multiflorum Lam.), an obligate outcrossing species, is widely cultivated due to its high biomass yield and good forage quality. Although Italian ryegrass is subject to intense selection activities within different breeding programs, stem rust caused by Puccinia graminis ssp. graminicola is still a major issue, especially during seed production. Stem rust infects leaf sheaths and inflorescences at the time of seed formation and consequently reduces seed yield. The increasing daily average temperatures due to climate change will further increase stem rust disease pressure. Until now, the knowledge on the genetic control of stem rust resistance in Italian ryegrass was limited. The aim of this study was to identify stem rust resistance genes within breeding material for efficient resistance breeding. We used a nested association mapping (NAM) population consisting of 708 F2 individuals, derived from crossing 23 diverse founders with one common founder, followed by an open pollination among F1 plants. Multisite field phenotyping as well as in vitro inoculation of leaf segments were conducted and revealed a high phenotypic variation for stem rust resistance. For genotyping, restriction site associated DNA sequencing resulted in 4,762,767 single nucleotide polymorphism (SNP) markers at affordable costs. Using all field phenotyping data combined with the genotypic data revealed three quantitative trait loci on chromosomes 6 and 7. On chromosome 7, SNPs significantly associated with resistance caused missense mutations within two receptor-like serine/threonine protein kinase predicted genes next to each other. Receptor-like serine/threonine protein kinases are known to confer resistance to many pathotypes of stem rust in other species such as barley. This study shows that a NAM population is suitable to find new resistance sources for stem rust in outcrossing species such as Italian ryegrass. Our findings can be either directly implemented by marker-assisted selection in breeding programs or used for functional validation of the candidate genes identified.
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species
Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland (2022)
Molecular Ecology Resources
Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within-species diversity) is related to many beneficial effects on the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large-scale assessments. However, the continuous advancement of high-throughput DNA sequencing approaches has improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost-effective method. Here, we report a set of 12 multispecies primer pairs that can be used for high-throughput PGD assessments in multiple grassland plant species. The target loci were selected and tested in two phases: a "discovery phase" based on a sequence capture assay (611 nuclear loci assessed in 16 grassland plant species), which resulted in the selection of 11 loci; and a "validation phase", in which the selected loci were targeted and sequenced using multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The multispecies amplicons had nucleotide diversities per species from 5.19 x 10(-3) to 1.29 x 10(-2), which is in the range of flowering-related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the primer pairs reported in this study provide the basis for large-scale, multispecies PGD monitoring in grassland plants.
Decoding Genetic Resistance to Stem Rust in Italian Ryegrass using a Nested Association Mapping Approach
Kiesbauer, Jenny; Grieder, Christoph; Sindelar, Meril; et al. (2024)
“Global Challenges for Crop Improvement” - Book of Abstracts
Italian ryegrass (Lolium multiflorum Lam.) is an obligate outcrossing fodder crop valued for its high biomass and good forage quality in Europe. Increasing daily average temperatures and decreasing precipitation due to climate change favor stem rust infections caused by Puccinia graminis ssp. graminicola. The fungal pathogen infects leaves and inflorescences at seed ripening stage and is therefore known to substantially reduce seed yield. The aim of this study was to find novel resistance sources within breeding material for efficient resistance breeding. We developed, for the first time in Italian ryegrass, a nested association mapping (NAM) population. The NAM population consists of 687 F2 individuals, derived from crossing 23 diverse founders with one common founder, followed by open pollination among the F1 progeny. For genotyping, double digest restriction-site associated (ddRAD) sequencing of the F2 population imputed with whole genome sequencing data of the founders revealed 3,199,253 single nucleotide polymorphisms (SNPs). For phenotyping, natural stem rust occurrence was assessed in three different field environments (each with two replicates) at seed harvest using a scale from 1 (no stem rust symptoms) to 9 (very heavy stem rust symptoms). A mixed linear model approach detected two loci, one on chromosome 6 and one on chromosome 7, significantly associated with stem rust. On chromosome 7 one SNP significantly associated with stem rust resistance was found within a gene predicted as a receptor like serine/threonine protein kinase. Serine/threonine protein kinases are known to be involved in stem rust resistance in species such as barley. This study showed that a NAM population is a valuable resource to find markers associated with disease resistance, which can be directly used for marker-assisted selection in the existing breeding program.
Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover
Frey, Lea A.; Vleugels, Tim; Ruttink, Tom; et al. (2022)
Theoretical and Applied Genetics
Key message High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
Sainfoin (Onobrychis viciifolia)
Nay, Michelle; Grieder, Christoph; Kölliker, Roland (2025)
Including marker x environment interactions improves genomic prediction in red clover (Trifolium pratense L.)
Skøt, Leif; Nay, Michelle M.; Grieder, Christoph; et al. (2024)
Frontiers in Plant Science
Genomic prediction has mostly been used in single environment contexts, largely ignoring genotype x environment interaction, which greatly affects the performance of plants. However, in the last decade, prediction models including marker x environment (MxE) interaction have been developed. We evaluated the potential of genomic prediction in red clover (Trifolium pratense L.) using field trial data from five European locations, obtained in the Horizon 2020 EUCLEG project. Three models were compared: (1) single environment (SingleEnv), (2) across environment (AcrossEnv), (3) marker x environment interaction (MxE). Annual dry matter yield (DMY) gave the highest predictive ability (PA). Joint analyses of DMY from years 1 and 2 from each location varied from 0.87 in Britain and Switzerland in year 1, to 0.40 in Serbia in year 2. Overall, crude protein (CP) was predicted poorly. PAs for date of flowering (DOF), however ranged from 0.87 to 0.67 for Britain and Switzerland, respectively. Across the three traits, the MxE model performed best and the AcrossEnv worst, demonstrating that including marker x environment effects can improve genomic prediction in red clover. Leaving out accessions from specific regions or from specific breeders’ material in the cross validation tended to reduce PA, but the magnitude of reduction depended on trait, region and breeders’ material, indicating that population structure contributed to the high PAs observed for DMY and DOF. Testing the genomic estimated breeding values on new phenotypic data from Sweden showed that DMY training data from Britain gave high PAs in both years (0.43–0.76), while DMY training data from Switzerland gave high PAs only for year 1 (0.70–0.87). The genomic predictions we report here underline the potential benefits of incorporating MxE interaction in multi-environment trials and could have perspectives for identifying markers with effects that are stable across environments, and markers with environment-specific effects.
Exploiting the Swiss Apple Core Collection for breeding tomorrow's apple cultivars
Broggini, Giovanni; Kölliker, Roland; Kellerhals, Markus; et al. (2023)
Acta Horticulturae ~ XXXI International Horticultural Congress (IHC2022): International Symposium on Conservation and Sustainable Use of Horticultural Genetic Resources
Plant genetic resources represent a valuable reservoir of genetic diversity that breeding programs can exploit. However, the number of inventoried accessions is usually large, and preservation and detailed description of all of them is laborious and expensive. Core collections represent a compact form to preserve the genetic diversity of crop species. In addition to mere preservation, a detailed description of the phenotypic diversity within core collections allows identifying accession-specific traits to be used efficiently in breeding programs. Replication of core collections at different locations can unravel genotype-by-environment interactions, which are relevant to understanding how climatic differences affect relevant traits. Especially in apple breeding, where genetic diversity in the few commercially successful varieties is low, broadening the genetic base is a crucial element to adapt cultivars to new challenges such as environmental changes or the occurrence of new pests and diseases as well as abiotic stress. To describe Swiss apple genetic resources and support apple breeding, the Swiss Federal Office for Agriculture initiated the establishment of a Swiss Apple Core Collection. It consists of 330 old Swiss apple varieties and accessions as well as 27 references. Three trees per genotype were planted at three climatically different locations each. The description of a broad range of traits, with the help of the latest phenotyping technologies, made it possible to identify variations for traits that will become important in the future. Priority was given to a detailed description of fruit quality features and tree performance. In a second project phase, attention will be given to diseases and abiotic stress tolerance. Combining high quality phenotypic information with genome-wide sequence data will allow identifying loci of interest and developing molecular markers associated with these. Including these traits in apple breeding programs will further enhance the development of diverse, resilient apple cultivars.
Sainfoin genomics: Unlocking the genetic potential of an underutilized crop
Pettersson, Alexander; Nay, Michelle; Studer, Bruno; et al. (2024)
Sainfoin (Onobrychis viciifolia Scop.) is a nutritious, drought-tolerant perennial forage legume with a long history in European pastures and meadows. Its high tannin content benefits different livestock species by controlling gastrointestinal nematodes in goats and sheep and reducing methane emissions and protein digestion in bovines. Despite these benefits, sainfoin cultivation declined in the mid-20th century due to the rise in popularity of more productive forage species like perennial ryegrass (Lolium perenne L.) and alfalfa (Medicago sativa L.). Today, sainfoin's re-establishment in Europe is hindered by a limited number of cultivars, low seed multiplication rates, and high seed costs, confirming its status as an underutilized forage legume. Addressing these limitations is important for its reintroduction, and genomics-assisted breeding tools can help expedite the improvement of key traits such as seed yield. Despite its beneficial qualities as a feed, there have been few projects aimed at developing genomic resources for sainfoin. High-quality reference genomes are important tools for genomics-assisted breeding, as they, for example, help researchers develop genetic markers that can be used in genome-wide association studies that link traits to specific genomic regions. Therefore, the first goal of my project is to assemble a phased chromosome-level reference genome for sainfoin using long- and short-read sequencing data. However, assembling a sainfoin genome is complicated by its autotetraploid genome, which requires resolving four homologous chromosomes. Similarly, its outcrossing mating system results in high genetic heterozygosity, increasing the risk of misassembly. To overcome these challenges, scaffolding techniques will be employed to phase the genome and achieve chromosome-level resolution. Reference genomes which represent the DNA of a single individual naturally miss many variants that contribute to trait diversity within a species. To address this, my research will focus on constructing a pan-genome by comparing gene content and structural variants across eight de novo assembled sainfoin genomes. Gene annotation and comparative analyses of the assembled genomes will identify core genes, present in all genotypes, and accessory genes, unique to specific genotypes, thereby providing a catalog of shared and unique regions across the sainfoin pan-genome. We anticipate that this resource will support genomics-assisted breeding programs aimed at producing improved sainfoin cultivars that are adapted to modern agriculture, ultimately promoting sainfoin’s reintroduction as a sustainable forage crop.

Publications 1 - 10 of 84

Roland Kölliker

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results