Biology subjects

AUBERT, G.

Publications and source records attributed to AUBERT, G..

4 recordsLinked to original sources

bioRxiv2025

A new genome assembly of the pea cultivar Cameor provides resources for functional genomics and genetics

Significant improvements in sequencing technologies have allowed the development of more contiguous genome assemblies in many plant species. The pea genome is characterized by its richness in repeated elements and its long and complex centromeres. This makes its assembly challenging. In this paper, we present an improved version of the genome sequence of the French cultivar Cameor. This sequence was obtained by combining Nanopore and PacBio long-read sequencing, Hi-C contact maps and Bionano maps. The assembly of centromeres was refined using a combination of FISH and ultra-long Nanopore read analyses. Overall, Cameor_v2 genome assembly is a highly continuous pea genome assembly with small total gap size and a large contig N50. In this version, the orientation of chromosomes was revised according to internationally accepted karyotype rules. Gene annotation statistics indicated a high completeness of gene sequences, with most gene sequences with 3 and 5 UTR. This genome assembly with its associated data constitute a useful resource for pea genetics, comparative mapping and functional genomics.

genomics↗

bioRxiv2025

QTL combinations associated with field partial resistance to aphanomyces root rot in pea Near-Isogenic Lines

Aphanomyces root rot, caused by Aphanomyces euteiches, is one of the most-important diseases of pea (Pisum sativum L.) worldwide. The development of resistant varieties is a major objective to manage the disease. Consistent quantitative trait loci (QTL) controlling partial resistance were discovered from linkage mapping and genome-wide association studies. This study aimed to validate the resistance QTL effects and identify effective QTL combinations under contaminated field conditions, by exploiting Near-Isogenic Lines (NILs) carrying resistance alleles at individual or combined consistent QTL in different genetic backgrounds. A total of 157 NILs previously created were fingerprinted using 10,494 SNP markers from the GenoPea Infinium(R) BeadChip, which made it possible to confirm the QTL introgression sizes in the NILs. All NILs were phenotyped for resistance in field contaminated nurseries over two years at six locations in France. NILs carrying resistance alleles from PI180693 or 90-2131 at the major-effect QTL Ae-Ps7.6, individually or in combination with minor-effect QTL (Ae-Ps4.1 or Ae-Ps5.1), showed significantly increased levels of partial resistance in different environments and genetic backgrounds. At other QTL combinations (Ae-Ps1.2 or AePs7.6 + Ae-Ps2.2 + Ae-Ps3.1), alleles from PI180693 or 552 also showed significant effects on partial resistance in some NIL genetic backgrounds. At these QTL combinations, the PI180693 resistance alleles also contributed to late flowering. This study provides tools and information for the choice of resistance QTL to combine in breeding, to increase partial resistance to A. euteiches in pea varieties.

genetics↗

bioRxiv2024

Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes

Cool-season grain legumes are mostly grown over spring and summer due to poor frost tolerance. However, fall-sown varieties often provide higher yields, earlier harvests and avoid late-season drought and heat. Understanding the genetic determinism and molecular basis of frost tolerance is therefore crucial for developing high-performing winter varieties. This study aimed to (1) investigate the genetic architecture of frost tolerance in Vicia faba L. using 247 accessions phenotyped under four field environments, and (2) explore the conservation of frost tolerance loci in cool-season legumes using the OrthoLegKB translational research database. A genome-wide association study identified nineteen V. faba genomic regions with a high density of markers significantly associated with frost tolerance, on all chromosomes. Mapping of frost tolerance QTL from V. faba and related species obtained from the literature onto their respective reference genomes and their integration into OrthoLegKB revealed synteny of major QTL across V. faba, Pisum sativum, and/or Medicago truncatula, particularly near clusters of CBF/DREB1 genes. Frost tolerance QTL at the P. sativum Le locus, which controls internode length, were also syntenic with a frost tolerance QTL in V. faba. Synteny between frost tolerance QTL and those controlling phenology and physiology was found at other loci, suggesting pleiotropy. Finally, expression data from P. sativum and C. arietinum accessions grown under low temperature were considered as information source to highlight potential candidate genes underlying the conserved QTL. Overall, these results provide a valuable resource for understanding and improving frost tolerance in V. faba and other cool-season legumes, including orphan crops by knowledge transfer. The use of OrthoLegKB to explore the genetic and molecular determinism of target traits across species is worth generalising.

plant biology↗

bioRxiv2022

SNP discovery by exome capture and resequencing in a pea genetic resource collection

Background & SummaryIn addition to being the model plant used by Mendel1 to establish genetic laws, pea (Pisum sativum L., 2n=14) is a major pulse crop cultivated in many temperate regions of the world. In order to face new challenges imposed particularly by global climate change and new regulations targeted at reducing chemical inputs, pea breeders have to take advantage of the genetic diversity present in the Pisum genepool to develop improved, resilient varieties. The aim of this study was to assess the genetic diversity of a pea germplasm collection and allow genome-wide association studies using this collection. To be able to perform genome-wide association approaches with high resolution, genotyping with a large set of genetic markers such as Single Nucleotide Polymorphism (SNP) markers well-spread over the genome is required. Rapid advances in second-generation sequencing technologies and the development of bioinformatic tools have revolutionized the access to and the characterization of available genetic diversity. High-density, high-throughput genotyping has been possible for a large number of species, including those with large and complex genomes2 such as pea (2n=14) which genome size is estimated to be 4.45 Gb3. In this study, which is part of the PeaMUST project4, we used a target capture technology based on pea transcriptome sequences to generate exome-enriched genomic libraries that were further subjected to Illumina sequencing in paired-end mode. This methodology was chosen because whole-genome resequencing is relatively expensive for species with large genomes and because capturing genetic variations in repeated non-coding regions is difficult to achieve or to interpret5. Whole-exome sequencing represented an interesting alternative that focused on coding regions only6,7. Mapping the obtained reads on the reference pea genome sequence enabled the discovery of an abundant set of SNPs. The development of this resource is a crucial cornerstone in research and breeding projects towards boosting the improvement of pea production and quality.

genomics↗