Biology subjects

Hinsinger, D.

Publications and source records attributed to Hinsinger, D..

4 recordsLinked to original sources

bioRxiv2026

Development and application of SNP markers to facilitate DUS testing in tomato

Variety registration in Europe requires the evaluation of Distinction, Uniformity, and Stability (DUS) based on multi-environment trials and extensive phenotyping. The integration of molecular markers into DUS testing offers opportunities to increase efficiency and reduce costs, particularly in tomato (Solanum lycopersicum L.), a species characterized by rapid varietal turnover. We developed a high-density SNP genotyping resource targeting gene-rich regions across the tomato genome and applied it to a panel of 300 varieties registered over the past five decades. Temporal patterns of genetic diversity were assessed and compared with those observed in a collection of heirloom accessions predating 1970. Genome-wide association studies (GWAS) were conducted for 50 DUS traits to identify marker-trait associations and evaluate the potential of SNPs to complement phenotypic descriptors. Detected associations were compared with previously reported genes and quantitative trait loci (QTLs), enabling the validation of known loci and the identification of novel candidate genomic regions underlying trait variation. Finally, we assessed the discriminatory power of selected subsets of informative SNPs for variety distinction and grouping. Our results demonstrate the potential of integrating genomic and phenotypic data to enhance the robustness, resolution, and scalability of DUS testing in tomato.

Plant Biology↗

bioRxiv2024

Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high- quality assemblies of five melon (Cucumis melo L.) accessions representing five diverse botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25x coverage for four of them multiplexed in half of a PromethION flowcell, and 48x coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Mercury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Mercury QV values ranging between 32 and 47. We focused on the complex NLR resistance gene clusters to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications. Article SummaryThis study presents high-quality nuclear, mitochondrial, and chloroplast genome assemblies for five diverse melon (Cucumis melo L.) accessions, using Oxford Nanopore sequencing. The assemblies represent a broad spectrum of melon diversity, including differences in origin, fruit morphology, or resistance traits. The genomes, ranging from 359 to 365 Mb, were assembled at a chromosome level with high contiguity, and verified using different validation approaches. This study provides valuable insights for research on melon genetic diversity, disease resistance, and breeding applications. The genome data will be especially valuable for plant geneticists, breeders, and researchers working on crop improvement and resistance traits.

genomics↗

bioRxiv2023

Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis melo L.)

BackgroundNanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept. ResultsWe showed that each of the 15 regions we identified in two newly assembled melon genomes (subspecies melo) were successfully and accurately reconstructed as well as in a third cultivar from the agrestis subspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In the agrestis cultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS. ConclusionsAltogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.

genomics↗

bioRxiv2019

The soursop genome and comparative genomics of basalangiosperms provide new insights on evolutionaryincongruence

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.

evolutionary biology↗