Biology subjects

Canaguier, A.

Publications and source records attributed to Canaguier, A..

5 recordsLinked to original sources

bioRxiv2026

Linkage and association mapping coupled with pan-genome analyses of Vat homologs reveal QTLs and alleles for aphid resistance in melon

Aphids threaten crop productivity through phloem feeding and the transmission of plant viruses. Aphis gossypii, in particular, is a widespread and damaging pest of worldwide cultivated melon. Resistance to its emerging CUC1 clone in Europe remains poorly characterized. Here, we dissected the genetic architecture of melon resistance to CUC1 using complementary traits that capture multiple stages of the aphid-melon interaction: plant attractiveness to aphids, acceptance, aphid colonization, and multiplication. Genome-wide association studies (GWAS) in a diversity panel of 174 accessions identified a quantitative trait locus (QTL) for attractiveness on chromosome 6, while analyses in a complementary panel of 212 accessions revealed QTLs for plant acceptance by aphids on chromosomes 3, 8, and 12. Colonization and multiplication traits further highlighted resistance QTLs on chromosomes 5 and 12, the latter supported by both SNP-based GWAS and bulk-segregant analysis. Pan-NLRome k-mer- and graph-based GWAS, together with Vat presence/absence association analyses, provided allele-level resolution of the QTL on chromosome 5, corresponding to the Vat region. Leveraging allelic diversity at this locus, we functionally characterized 20 Vat homologs with four R65aa motifs within their leucine-rich repeat (LRR) domain and demonstrated the capacity of 4R65aa-type Vat alleles to confer clone-specific resistance. Resistance-conferring alleles limited virus multiplication, such as Cucumber mosaic virus (CMV), when transmitted by five A. gossypii clones, including CUC1. Together, our results revealed multiple genetic determinants underlying quantitative resistance to the A. gossypii CUC1 clone in melon and highlighted the central role of Vat homologs in resistance to both A. gossypii and the viruses it vectors. These findings provide strategic targets for pyramiding resistance loci acting at different stages of the pest life cycle to enhance durable protection against these biotic threats.

genetics↗

bioRxiv2025

Intra-specific NLR allelic diversity and genomic landscape for plant resistance association studies

The identification of nucleotide-binding domain leucine-rich repeat receptor genes (NLRs) across multiple accessions is essential to capture their genetic diversity within a plant species. Using Nanopore adaptive sampling and de novo assembly, we accurately reconstructed the NLR regions across 143 Cucumis melo accessions representing diverse botanical groups and geographical origins. NLR annotation evidenced diverse cluster architectures and unexpected variation in NLR content across accessions, leading to unsaturated allelic diversity curves. Using this diversity, we further proposed pan-NLRome graph- and k-mer-based genome-wide association studies (GWAS), which, using Fusarium wilt races 1 and 2 severity data, accurately identified Fom-1, Fom-2, and novel non-NLR candidates. Furthermore, we extended these approaches for the identification of a candidate gene for flaccid necrosis caused by zucchini yellow mosaic virus. Our study offers a comprehensive view of NLR diversity in melon, overcoming the limitations of single-reference analyses, and supporting future efforts in NLR-focused GWAS and resistance breeding.

genomics↗

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↗

bioRxiv2021

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection.

BackgroundStructural Variations (SVs) are very diverse genomic rearrangements. In the past, their detection was restricted to cytological approaches, then to NGS read size and partitionned assemblies. Due to the current capabilities of technologies such as long read sequencing and optical mapping, larger SVs detection are becoming more and more accessible. This study proposes a comparison in SVs detection and characterization from long-read sequencing obtained with the MinION device developed by Oxford Nanopore Technologies and from optical mapping produced by the Saphyr device commercialized by Bionano Genomics. The genomes of the two Arabidopsis thaliana ecotypes Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1) were chosen to guide the use of one or the other technology. ResultsWe described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 on the public reference Col-0 TAIR10.1. After filtering, 1 184 and 591 Ler-1 SVs were retained from ONT and BioNano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations in both technologies. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. ConclusionsStructural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference, most of detected SVs were found in same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the later being more efficient to characterize large SVs. Even if both technologies are obvious complementary approaches, ONT data appears to be more adapted to large scale populations study, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.

genomics↗