Biology subjects

Visser, R. G. F.

Publications and source records attributed to Visser, R. G. F..

9 recordsLinked to original sources

bioRxiv2025

Two high-quality rose genomes underpin a novel Rosa pangenome to advance rose genomics, phylogenetics, and breeding

Rosa, belonging to the family Rosaceae, encompasses more than 150 species which are widely distributed in the northern hemisphere. Renowned for their beauty, roses are cultivated throughout the world for ornamental purposes and the production of essential oils and perfumes. Despite their cultural and commercial significance, the genomic resources of wild Rosa species have not been studied comprehensively, hampering the understanding of their genetic diversity, evolutionary history, and breeding potential. Here we report on high-quality de novo genomes for Rosa sericea and Rosa rugosa. By integrating these two de novo genomes with existing public genomic resources, we have built a Rosaceae panproteome and a Rosa pangenome (spanning wild, traditional garden, and modern rose lineages) using a De Bruijn graph (DBG)-based approach. A maximum likelihood (ML) phylogeny of 18 Rosa haplotypes based on 4,367 single-copy core homology groups (genes) provided robust evolutionary inference, confirming the basal position of R. sericea, and enabled a gene-based macrosynteny analysis across the pangenome. Our analyses revealed significant genomic diversity among species, extensive variation in core gene content, and lineage-specific transposable element (TE) expansion patterns that contribute to the variation in Rosa genome size and to species-specific adaptations. The pangenome also revealed biased diversification of homology groups potentially linked to phenotypic plasticity in Rosa. Specifically, our analysis of the rose scent-related gene family, NUDX1, uncovered its evolutionary trajectory in Rosa, in which TEs insertions provided putative novel regulatory elements that facilitated adaptive evolution in metabolic pathways. This pangenomic study deepens our understanding of the genetic diversity and evolution of traits within the Rosa genus. In addition, the findings lay the foundation for future efforts to understand the genetic mechanisms driving trait evolution, which can support rose breeding.

genomics↗

bioRxiv2024

CRISPR/Cas9-induced breaks are insufficient to break linkage drag surrounding the ToMV locus of Solanum lycopersicum

Despite the success of CRISPR/Cas9 in inducing DNA double-strand breaks (DSBs) for genome editing, achieving targeted recombination in somatic cells remains challenging, particularly at recombination cold spots like the Tomato Mosaic Virus (ToMV) resistance locus in Solanum lycopersicum. We investigated the potential of CRISPR/Cas9-induced targeted recombination in somatic cells to overcome linkage drag surrounding the ToMV locus. We employed two strategies: first, inducing DSBs in both alleles of F1 tomato seedlings to promote non-homologous end joining (NHEJ) and homology-directed repair (HDR); second, targeting a single allele in a heterozygous background to induce HDR in seedlings. CRISPR/Cas9 activity was confirmed in F seedlings by detecting NHEJ-mediated mutations at the target sites in ToMV. We developed a bioinformatics pipeline to identify targeted recombinants by analyzing single nucleotide polymorphisms (SNPs) between parental haplotypes, allowing precise tracking of SNP variations. A two-dimensional pooling strategy was employed to distinguish genuine recombination events from PCR artifacts. Despite these advances and the active CRISPR/Cas9 system in F1 progeny, no increase in recombination frequency was observed compared to wild-type plants. We extended our research to protoplasts to assess whether CRISPR/Cas9 could induce targeted recombination under different cellular conditions at the same locus. Consistent with our findings in F1 plants, we observed no increase in recombinant patterns compared to wild-type controls in protoplasts. Our findings suggest that CRISPR/Cas9-induced DSBs are insufficient to break the genetic linkage at the ToMV locus on chromosome 9 in recombination cold spots within somatic cells. Article SummaryThis research targets plant biologists and geneticists interested in enhancing plant breeding techniques. The study used CRISPR/Cas9 technology to induce DNA breaks in tomato plants. It specifically targeted the Tomato Mosaic Virus (ToMV) resistance gene, which resists natural recombination. The aim was to induce genetic recombination via CRISPR/Cas9. The highly active CRISPR/Cas9 system did not increase the expected genetic changes, indicating challenges in achieving targeted recombination. These findings highlight the challenges in breaking genetic linkages in specific genome regions using current CRISPR methods. These findings are relevant for developing techniques for targeted recombination in plant breeding.

molecular biology↗

bioRxiv2024

Key determinants of CRISPR/Cas9 induced inversions in tomato

Inversions in chromosomes occur widely within plants and suppress meiotic recombination which can be beneficial or detrimental for plant breeders. Therefore, induction or reversion of inversions via CRISPR/Cas9 has been extensively researched recently. Extensive variation in inversion induction rates and sizes have been reported, from hundreds to several million base pairs. Here, we dissect the influential factors of inversion induction efficiency using CRISPR/Cas9. By using a fixed reference gRNA, we could directly correlate gRNA mutation frequency to inversion frequency and inversion size, of inversions up to 37.5 Mb in length in tomato. Our findings indicate that the least efficient gRNA is the bottleneck for inversion induction, with inversion size having no significant influence unless the inversions were larger than 1 Mb in size. For these huge inversions, the frequency dropped astoundingly, regardless of the gRNA cutting efficiencies. We hypothesize an in planta yet unknown variant of non-homologous-end-joining (NHEJ)-based repair which utilizes active transport of damaged chromosomal sections to dedicated repair sites in the cell nucleus, where repair is finalized. We propose that large inversions are formed less frequently because the transport of these segments to the repair sites may be hampered by their sheer size.

molecular biology↗

bioRxiv2023

Chromosome level assembly of wild spinach provides insights into the divergence of homo- and heteromorphic plant sex-chromosomes.

BackgroundCultivated spinach (Spinacia oleracea) is a highly nutritional crop species of great economical value that belongs to a genus of dioecious plant species with both homomorphic and heteromorphic sex chromosomes. The wild spinach species Spinacia turkestanica and Spinacia tetrandra are important genetic sources for improving cultivated spinach and excellent material for studying sex chromosome evolution in plants. However, until now there were no publicly available genome assemblies for these species. ResultsHere we sequenced and assembled the genomes of S. turkestanica and S. tetrandra and performed a tri-way comparative analysis with S. oleracea. We show that many abiotic- and biotic stress related gene clusters have expanded through tandem duplication in S. tetrandra after it diverged from the S. turkestanica - S. oleracea lineage. Focussing on the sex chromosomes we found that the previously identified inversion distinguishing the S. oleracea male- and female-SEX DETERMINING REGIONs (SDRs) is conserved in S. turkestanica. Although, the SDRs of these two species coincides with the PSEUDO AUTOSOMAL REGION of S. tetrandra the gene content is only partially conserved and the genetic factors determining sex in these species might differ. Finally, we show that recombination suppression between the S. tetrandra X- and Y-chromosomes resulted in a highly degenerated Y-chromosome and started before the species diverged from S. turkestanica and S. oleracea. ConclusionsWe expect that the novel wild spinach species genomes are of great value to the breeding community and evolutionary biologist especially focussing on the evolution of sex chromosomes in plants.

evolutionary biology↗

bioRxiv2023

Desynapsis in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility

The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers. A strong reduction of crossovers leads to desynapsis, a process in which pairing of homologous chromosomes is abolished before metaphase I. This results in a random segregation of univalent and the production of unbalanced and sterile gametes. However, if desynapsis is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced gametes, essentially composed of non-recombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, desynapsis is a recessive trait that was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the desynapsis locus and identified StMSH4, an essential component of the class I crossover pathway, as the most likely candidate gene. A seven base-pair insertion in the second exon of StMSH4 was found to be associated with desynapsis in our mapping population. We also identified a second allele with a 3820 base-pair insertion and confirmed that both alleles cannot complement each other. Such non-functional alleles appeared to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove desynaptic alleles from their germplasm to improve fertility or to use them to produce highly uniform unreduced gametes in alternative breeding schemes.

plant biology↗

bioRxiv2022

Tetraose glycoalkaloids from potato can provide complete protection against fungi and insects

Plants with innate disease and pest resistance can contribute to more sustainable agriculture. Natural defence compounds produced by plants have the potential to provide a general protective effect against pathogens and pests, but they are not a primary target in resistance breeding. Here, we identified a wild relative of potato, Solanum commersonii, that provides us with unique insight in the role of glycoalkaloids in plant immunity. We cloned two atypical resistance genes that provide resistance to Alternaria solani and Colorado potato beetle through the production of tetraose steroidal glycoalkaloids. Moreover, we provide in vitro evidence to show that these compounds have potential against a range of different (potato pathogenic) fungi. This research links structural variation in steroidal glycoalkaloids to resistance against potato diseases and pests. Further research on the biosynthesis of plant defence compounds in different tissues, their toxicity, and the mechanisms for detoxification, can aid the effective use of such compounds to improve sustainability of our food production.

plant biology↗

bioRxiv2021

De novo whole-genome assembly of Chrysanthemum makinoi, a key wild ancestor to hexaploid Chrysanthemum

Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The wild diploid Chrysanthemum makinoi is thought to be one of the ancestors of the cultivated hexaploid varieties which are currently grown all around the world. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences and a genetic map, we assembled 3.1 Gb of its sequence into 9 pseudochromosomes, with an N50 of 330 Mb and BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95 074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution and history.

genomics↗

bioRxiv2021

Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

MotivationThe investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. ResultsHere we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availability and implementationpolyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Contactpeter.bourke@wur.nl or chris.maliepaard@wur.nl Supplementary informationSupplementary data are available

genetics↗

bioRxiv2017

polymapR: linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

MotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the worlds most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.\n\nResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.\n\nAvailability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.\n\nContactChris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl

genetics↗