Daniela Kupper


Last Name

Kupper

First Name

Daniela

ORCID

0009-0009-7128-290X

Organisational unit

03969 - Studer, Bruno / Studer, Bruno

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2024 - 20255
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Publications 1 - 5 of 5
  • From sequence to cross-compatibility prediction: a functional analysis of self-incompatibility haplotypes in forage grasses
    Item type: Other Conference Item
    Kupper, Daniela; Manzanares, Chloé; Rohner, Marius; et al. (2025)
    Breeding and Genetic Improvement for a Net-Zero Future - Abstracts of the 36th Meeting of the EUCARPIA Fodder Crops and Amenity Grasses Section
    Hybrid breeding forms the basis of seed production for many crop species. In forage grasses, however, self-pollination and inbred line production are naturally prevented by gametophytic self-incompatibility (SI), a genetic mechanism that promotes outcrossing. In grasses, SI is controlled by two multi-allelic loci, S and Z. At each locus, three genes are involved in self-recognition: two genes encoding a transmembrane protein (DUF247) expressed in the pollen, and one gene encoding a small, secreted peptide expressed in the stigma. Yet, knowledge of their sequence diversity, allelic variation and physiological functions remains limited. Understanding how these genes interact to regulate SI could unlock opportunities to control pollination and support the development of hybrid breeding strategies. To build a model predicting cross-compatibility based on genotypic data, we established an F1 population of perennial ryegrass (Lolium perenne L.), derived from a polycross of five parental plants. Consequently, the population comprises a restricted number of haplotypes at the two SI loci S and Z. To identify the different SI alleles present within the population, we used a probe capture assay, followed by next-generation sequencing and de novo assembly of alleles. Based on the translated amino acid sequence, we clustered the different SI alleles with 99% similarity to form putative SI haplotypes. To link the genotypic data to phenotypic data from semi-in vivo pollination assays, we performed more than 2,900 targeted crosses between 30 plants within the F1 population in 2023 and 2024: an example semi-in vivo pollination is shown in Figure 1. Currently, we are repeating the crosses for a subset of ten genotypes, for which we were able to fully recover the putative SI haplotypes at both loci. This fully characterized subset was used to train a model for cross-compatibility predictions. We were able to assess the overlap between the predicted cross-compatibility and the observed cross-compatibility in the 2023 crosses. In 30 out of 58 crosses, the predicted and observed cross-compatibility was identical. However, twelve crosses deviated by at least 50% in observed cross-compatibilities. By analyzing the phenotypic data from 2024 and 2025, we seek to better understand the sources of variation between the predicted and observed cross-compatibility. Ultimately, we aim to define which sequence characteristics of the SI alleles determine SI recognition, with a view to defining functional haplotypes. This knowledge would enable the development of a tool for breeders to assess the allelic diversity of SI in their breeding pool and to predict cross-compatibility between genotypes.
  • Towards restoring self-incompatibility in inbred crops – a pilot study in Brachypodium distachyon
    Item type: Other Conference Item
    Kupper, Daniela; Kupper, Daniela; Manzanares, Chloe; et al. (2025)
    Self-incompatibility (SI) is present in over half of the angiosperms. It serves to promote outcrossing and increase genetic diversity in plant populations. In allogamous Poaceae species, SI is governed by a unique gametophytic system based on two multi-allelic loci, S and Z. Rohner et al. (2023) identified the genes responsible for the initial self-recognition in perennial ryegrass (Lolium perenne L.). Both the S and the Z loci comprise three genes: two pollen-expressed genes encoding a transmembrane protein (DUF247, male determinants) and one stigma-expressed secreted peptide (female determinant). Using Brachypodium distachyon (L.) as a model, we aim at restoring SI in this otherwise self-compatible grass species, thereby providing functional validation of the SI genes identified in L. perenne. The six SI genes, along with the native promoters of two, were cloned into a single 40.3 kb DNA vector construct for stable plant transformation. Transcriptional reporter lines containing mCitrine are also being developed to confirm spatio-temporal expression in B. distachyon. Preliminary results show that the promoter of the female SI component from L. perenne is driving stigma-specific expression in B. distachyon. These results provide a first indication of the feasibility of restoring SI by transferring L. perenne genes into B. distachyon. Using B. distachyon will allow us to bypass the vernalization and transformation bottlenecks in L. perenne and accelerate studies of the physiological and biological mechanisms underlying SI in grasses. Moreover, these studies will set a precedent for restoring SI in other crop species and bring new tools for plant breeders. References: Rohner M., Manzanares C., Yates S., Thorogood D., Copetti D., Lübberstedt T., Asp T., and Studer B, 2023. Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses. Mol Biol Evol. 40 (1).
  • Evaluation of genomic and phenomic prediction for application in apple breeding
    Item type: Journal Article
    Jung, Michaela; Hodel, Marius; Knauf, Andrea; et al. (2025)
    BMC Plant Biology
    BackgroundApple breeding schemes can be improved by using genomic prediction models to forecast the performance of breeding material. The predictive ability of these models depends on factors like trait genetic architecture, training set size, relatedness of the selected material to the training set, and the validation method used. Alternative genotyping methods such as RADseq and complementary data from near-infrared spectroscopy could help improve the cost-effectiveness of genomic prediction. However, the impact of these factors and alternative approaches on predictive ability beyond experimental populations still need to be investigated. In this study, we evaluated 137 prediction scenarios varying the described factors and alternative approaches, offering recommendations for implementing genomic selection in apple breeding.ResultsOur results show that extending the training set with germplasm related to the predicted breeding material can improve average predictive ability across eleven studied traits by up to 0.08. The study emphasizes the usefulness of leave-one-family-out cross-validation, reflecting the application of genomic prediction to a new family, although it reduced average predictive ability across traits by up to 0.24 compared to 10-fold cross-validation. Similar average predictive abilities across traits indicate that imputed RADseq data could be a suitable genotyping alternative to SNP array datasets. The best-performing scenario using near-infrared spectroscopy data for phenomic prediction showed a 0.35 decrease in average predictive ability across traits compared to conventional genomic prediction, suggesting that the tested phenomic prediction approach is impractical.ConclusionsExtending the training set using germplasm related with the target breeding material is crucial to improve the predictive ability of genomic prediction in apple. RADseq is a viable alternative to SNP array genotyping, while phenomic prediction is impractical. These findings offer valuable guidance for applying genomic selection in apple breeding, ultimately leading to the development of breeding material with improved quality.
  • Unravelling the genetics of self-incompatibility in grasses
    Item type: Conference Poster
    Kupper, Daniela; Manzanares, Chloe; Studer, Bruno (2024)
    Self-incompatibility (SI) is a genetically controlled mechanism present in more than half of the Angiosperms. It prevents the mating of individuals with similar genetic backgrounds and therefore promotes outcrossing. A highly effective SI system can be found widespread within grasses (Poaceae), one of the most economically important plant families. The outcrossing nature, especially common within forage grasses, limits breeding methodologies that can be applied (e.g., hybrid breeding) and is partially responsible for the low genetic gain observed over the last decades. The grass SI system is governed by two multi-allelic loci, S and Z. Each locus contains three genes thought to be involved in the self-recognition in perennial ryegrass (Lolium perenne L.). These genes that we recently identified have not yet been functionally validated, and only limited knowledge exists about their sequence diversity, their allelic richness, and their physiological function. This project aims to confirm the SI determinants by a gain-of-function and a loss-of-function approach. The SI genes from perennial ryegrass will be brought into the self-compatible model plants Brachypodium distachyon (L.) and Arabidopsis thaliana through genetic transformation. The loss-of-function project will be conducted in Italian ryegrass (L. multiflorum Lam.) through a TILLING approach (Targeting Induced Local Lesion IN Genomes). In parallel, using targeted resequencing in a large collection of perennial and Italian ryegrass, as well as other forage grasses, we aim to gain knowledge about the allelic diversity and the evolution of this SI mechanism. Lastly, we will link the allelic diversity of the SI determinants to pollination compatibility, using a semi in-vivo pollination assay in a restricted number of plants sharing common ancestors. This knowledge will help to predict cross-compatibility and, therefore, has a practical use in grass breeding.
  • Gametophytic self-incompatibility in grasses: understanding a unique mechanism of pollen-pistil interaction
    Item type: Other Conference Item
    Manzanares, Chloé; Rohner, Marius; Yates, Steven; et al. (2024)
    27th International Congress on Sexual Plant Reproduction Program and Abstract Book
    Self-incompatibility (SI), a mechanism preventing self-pollination, has been intensively studied over the past 60 years among angiosperms. In grasses, we recently identified the genes responsible for the recognition of self-pollen by the pistil (Rohner et al, 2023). This unique grass SI system is governed by two multi-allelic loci, S and Z, each containing three genes. For each locus, two genes expressed in pollen, annotated as containing a domain of unknown function (DUF) 247, encode for transmembrane proteins (LpSDUF247-I and LpSDUF247-II at the S-locus, LpZDUF247-I and LpZDUF247-II at the Z-locus). The third gene, expressed in stigma, is coding for a small protein, predicted to be secreted (LpsS and LpsZ). Upon pollination, pollen grains sharing common SI haplotypes at both loci with the stigma will show a rapid pollen tube growth arrest, prior to stigma penetration in most cases. Here we report the results of a large targeted sequencing project of hundreds of samples, revealing high allelic diversity at the SI genes, a characteristic feature of SI determinants. These results, combined with protein folding predictions, provide insight into functional mechanisms. In addition, we report the latest results looking beyond the initial pollen-stigma recognition governed by S and Z. Through comprehensive genetic mapping in Lolium perenne, we have identified genomic regions, distinct from S and Z, which are associated with self-compatibility phenotypes. Subsequent gene identification and protein characterization within these regions will provide insights into the molecular mechanisms driving self-pollen recognition and the downstream SI response. Our findings shed light on the complex genetic architecture of SI in L. perenne and offer new perspectives on the evolutionary dynamics of SI systems in flowering plants.
Publications 1 - 5 of 5