Biology subjects

Brault, M.

Publications and source records attributed to Brault, M..

4 recordsLinked to original sources

bioRxiv2026

Postharvest tomato shelf life is genetically distinct from fruit firmness: evidence from two F2 populations

Reducing postharvest fruit loss without compromising fruit quality is a major goal in tomato breeding. Fruit shelf life is a complex trait, influenced by postharvest changes in fruit firmness and weight, as well as by both genetic and environmental factors. A QTL mapping experiment was conducted to identify loci associated with fruit shelf life-related traits using two distinct F2 tomato populations. Fruit weight, firmness, shelf life (evaluated as both loss of fruit weight and loss of firmness over time), and colour space components were measured, and QTLs were mapped using a commercial low-density SNP genotyping panel and bulk segregant sequencing analysis experiments. We show that fruit firmness at harvest is only weakly predictive of postharvest firmness loss, indicating that shelf life should be treated as a dynamic trait rather than a static firmness phenotype. Across the two populations, 60 QTLs defining 26 genomic regions were identified, including both population-specific loci and shared regions on chromosomes 9 and 12. Several narrow intervals contained candidate genes related to ethylene signaling, cell-wall remodeling, calcium transport, aquaporin-mediated water balance and stress responses. The identified QTLs and candidate genes are directly relevant to breeding programmes seeking to improve postharvest performance without using major ripening mutants that compromise fruit quality. Key messageComparative QTL mapping and BSA-Seq in two F2 tomato populations show that postharvest shelf life is only partly explained by fruit firmness at harvest and identify candidate loci for firmness loss and weight loss during storage.

plant biology↗

bioRxiv2025

Evolution of crop phenotypic spaces through domestication

O_LIWe used domestication as an in vivo replicated experiment to investigate how divergent selection has shaped the evolution of multivariate phenotypic spaces. C_LIO_LIWe measured 11 to 57 qualitative and quantitative traits in 13 species, either unique or shared between species, and established a framework for cross-species comparisons. C_LIO_LIOur results revealed significant convergence that translated into a cross-species domestication syndrome. Most species exhibited a reduction of the multivariate phenotypic space during domestication. We brought evidence that Near Infrared spectra measured on leaves reflect phenotypic evolution unrelated with domestication, enabling its use as a control for sampling effects across species. Building on this, we developed a multivariate Phenotypic Divergence Index (mPDI) to rank species by the extent of phenotypic divergence under domestication. We found a high disjunction of wild and domestic phenotypic spaces in all species. Neither the mPDI nor the relative size of wild versus domestic multivariate phenotypic spaces was influenced by the domestication timing or mating system. Lastly, we observed a progressive decoupling of trait correlations with increasing time since domestication. C_LIO_LIIn addition to introducing a new index that can be applied for cross-species comparisons, our study uncovers recurring patterns shared among species, pointing to general principles underlying plant domestication. C_LI

evolutionary biology↗

bioRxiv2025

Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing

The effect of natural selection on linked sites has been suggested to be a major determinant of genetic diversity. While it is in principle possible to estimate this effect from genome sequence data, interactions between selection, demography and inbreeding are expected to make inference less reliable. Here we investigate whether the genome-wide reduction in diversity due to background selection ([B]) can be accurately estimated when populations are at demographic non-equilibrium and/or reproduce by partial self-fertilisation. We show that the classic-BGS model is surprisingly robust to both demographic non-equilibrium and low rates of selfing, although both processes do lead to biased estimation of the distribution of fitness effects (DFE) of deleterious mutations. A high rate of selfing leads to poor estimation of both[B] and DFE parameters. We propose an alternative inference approach where background selection, demography and partial selfing are jointly estimated from windowed site frequency spectra. This approach, while approximate in nature, resolves most of the bias observed under the classic-BGS model and can also generate estimates of past demography that account for the effect of background selection and partial selfing. We apply the approach to genome sequence data from Capsella grandiflora and C. orientalis, which have contrasting mating systems and display a forty-fold difference in nucleotide diversity. Our results suggest that background selection has a weak effect on levels of genetic diversity in the outcrosser C. grandiflora ([B] = 0.89) and a more substantial effect in the predominantly selfing species C. orientalis ([B] = 0.44), but that background selection alone cannot explain their disparity in genetic diversity.

evolutionary biology↗

bioRxiv2023

Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency

Optimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintain crop yield and reduce environmental pollution. This study aimed at identifying quantitative trait loci (QTL) and differential expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterised a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven (27) QTLs were detected for three target traits (Leaf N content, leaf Nitrogen Balance Index and petiole NO3- content), ten and six at low and high N condition, respectively; while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4,752 and 2,405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3,628 (50.6%) in leaves and 1,717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1,677 DEGs were shared between organs or tissues. Finally, we integrated DEGs and QTLs analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding improved-NUE tomato. HighlightTomato response to nitrogen deficiency is genetically controlled by a few QTLs and impacts the expression of a large number of genes, among which some are good targets for breeding sober varieties.

plant biology↗