Biology subjects

Esselink, D.

Publications and source records attributed to Esselink, D..

4 recordsLinked to original sources

bioRxiv2026

Development of the 4TREE SNP array, a forest multispecies array to enhance European Breeding and conservation programs in pine, poplar and ash.

Within the framework of the European Adaptive BREEDING for Better FORESTs project (B4EST, https://b4est.eu/), we have developed genotyping tools for Poplar, Ash, and Pine forest tree species. SNP arrays are attractive genotyping tools because of the user-friendly genotype calling system and the robust transferability among laboratories. Here we describe the development of an Axiom SNP array for Pinus pinaster (13,407 SNPs), Pinus pinea (5,671 SNPs), Poplar spp. (13,408 SNPs), and Fraxinus spp. (13,407 SNPs) based on a two-step process. We first assembled a high-density (>100,000 SNPs/species) screening array that served to test a large panel of candidate SNPs on a diversity panel involving at least 120 individual trees per species or species group. In the second step, we selected and combined the most informative SNPs to build the final 50,000 SNP 4TREE array. This approach resulted in high genotyping success rates, including for species lacking previously validated high-quality SNP resources. The 4TREE SNP array provides a valuable and transferable genomic tool to support genomic prediction, breeding, and adaptive management of forest tree species.

genomics↗

bioRxiv2025

Mutation or deletion of the Avr6 avirulence effector gene of Fulvia fulva leads to breakdown of the Cf-6 leaf mold resistance locus in tomato

Genetic resistance mediated by Cf cell-surface receptors is a cornerstone of tomato breeding against leaf mold disease caused by the fungal pathogen Fulvia fulva. After widespread deployment of the Cf-9 resistance locus, breeders increasingly relied on Cf-6, yet Cf-6-mediated resistance has already been overcome in multiple regions. The molecular basis of this breakdown, and the identity of the matching avirulence (Avr) effector, have remained unresolved. Here, we use comparative genomics and functional genetics to identify the F. fulva effector Avr6 as the previously described apoplastic protein Ecp5. Sequencing of Cf-6-breaking strains revealed either deletion of the Ecp5 locus or non-synonymous mutations in its coding sequence. Using transient expression, targeted gene knockout, and complementation assays, we show that Ecp5 is both necessary and sufficient for Cf-6-mediated recognition and defence activation. We then use Avr6-triggered cell death as a phenotypic marker in a bulked segregant analysis combined with Comparative Subsequence Sets analysis (CoSSa) to map Cf-6 to a [~]2 Mb interval on the short arm of chromosome 12 that overlaps the previously described Cf-Ecp5.12 locus. Sequencing of Avr6 in a broad strain collection reveals a predominantly conserved allele under apparent purifying selection, with recent independent loss-of-function variants in Europe and South America that confer virulence on Cf-6 plants. Together, these findings establish the Avr6-Cf-6 gene-for-gene pair, explain the erosion of Cf-6-mediated resistance, and illustrate how effector loss or mutation provides a rapid route for F. fulva adaptation, with important implications for designing more durable resistance strategies against tomato leaf mold.

microbiology↗

bioRxiv2025

High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

We present the first reference genome of highly heterozygous autotetraploid Allium porrum (leek). Combining long-read sequencing with SNP-array screening of two experimental F1 populations, we generated a genetic map with 11,429 SNP markers across 8 linkage groups and a chromosome-scale assembly of Allium porrum (leek) totaling 15.2 Gbp in size. High quality of the reference genome is substantiated by 97.2% BUSCO completeness and a mapping rate of 96% for full-length transcripts. The linkage map exposes the recombination landscape of leek and confirms that crossovers are predominantly proximal located to the centromeres, contrasting with distal recombination landscapes observed in other Allium species. Comparative genomics revealing structural rearrangements between A. porrum and its relatives (A. fistulosum, A. sativum, A. cepa), suggests a closer genomic relationship to A. sativum. Our annotated high-quality reference genome delivers crucial insights into the leek genome structure, recombination landscape, and evolutionary relationships within the Allium genus, offering significant implications for breeding programs, facilitating marker-assisted selection and genetic improvement in leek.

plant biology↗

bioRxiv2022

DNA primase large subunit is an essential plant gene for geminiviruses, putatively priming viral ss-DNA replication

The family of Geminiviridae consists of more than 500 circular single-stranded (ss) DNA viral species that can infect numerous dicot and monocot plants. Geminiviruses replicate their genome in the nucleus of a plant cell, taking advantage of the hosts DNA replication machinery. For converting their DNA into double-stranded DNA, and subsequent replication, these viruses rely on host DNA polymerases. However, the priming of the very first step of this process, i.e. the conversion of incoming circular ssDNA into a dsDNA molecule, has remained elusive for almost 30 years. In this study, sequencing of melon (Cucumis melo) accession K18 carrying the Tomato leaf curl New Delhi virus (ToLCNDV) recessive resistance quantitative trait locus (QTL) in chromosome 11, and analyses of DNA sequence data from 100 melon genomes, showed a conservation of a shared mutation in the DNA Primase Large subunit (PRiL) of all accessions that exhibited resistance upon a challenge with ToLCNDV. Silencing of (native) Nicotiana benthamiana PriL and subsequent challenging with three different geminiviruses showed a severe reduction in titers of all three viruses, altogether emphasizing an important role of PRiL in geminiviral replication. A model is presented explaining the role of PriL during initiation of geminiviral DNA replication, i.e. as a regulatory subunit of primase that generates an RNA primer at the onset of DNA replication in analogy to DNA Primase-mediated initiation of DNA replication in all living organisms.

plant biology↗