Biology subjects

Tiret, M.

Publications and source records attributed to Tiret, M..

8 recordsLinked to original sources

bioRxiv2025

The Paraphyletic Origins of Genetic Resistance to Cabbage Stem Flea Beetle in Brassica oleracea

The cabbage stem flea beetle (CSFB) poses a growing threat to winter Brassica crops in Europe, yet the genetic basis of resistance remains poorly understood. To clarify the genetic architecture and evolutionary origins of resistance to CSFB adult feeding, we conducted a genome-wide association study (GWAS) by combining high-throughput pool-sequencing and a large-scale non-choice feeding assay on 113 Brassica oleracea accessions from wild (or feral) populations and major domesticated morphotypes. We demonstrate that resistance displays moderate heritability with a predominantly polygenic basis, revealing strong phenotypic divergence among morphotypes: B. oleracea var. capitata was generally susceptible, whereas var. botrytis and wild populations showed markedly higher resistance. Despite this polygenic background, we identified a major-effect candidate QTL on chromosome C01 with strong enrichment of resistance alleles in wild populations and susceptible alleles in var. capitata. Genome-wide F-statistics and heterozygosity scans revealed a recent selective sweep at this locus in wild lineages. Considering current evidence for the feral origin of contemporary "wild" populations, our results suggest that resistance evolved after domestication and subsequent feralization, independently of resistance in var. botrytis. This paraphyletic distribution underlines the critical importance of integrating demographic history into quantitative genetic analyses of domesticated plant systems.

genetics↗

bioRxiv2024

An unexplored diversity for adaptation of germination to high temperatures in Brassica species

Elevated temperatures inhibit the germination of a concerning number of crop species. One strategy to mitigate the impact of warming temperatures is to identify and introgress adaptive genes into elite germplasm. Diversity must be sought in wild populations, coupled with an understanding of the complex pattern of adaptation across a broad range of landscapes. By investigating the landraces, wild, and feral populations of Algeria, Italy, France, Slovenia, Spain, and Tunisia, we assessed the response of germination to temperature increase in an unexplored diversity of 117 accessions of B. rapa and 66 of B. oleracea. Our results show that both species exhibit heat tolerance to the temperature range tested, especially B. rapa with an increase in speed and uniformity of germination time, as well as an increase in germination rate as temperature increased. As for B. oleracea accessions, the ability to germinate under heat conditions depended on the geographical origin; in particular, southern populations showed a higher germination rate than northern populations, possibly in relation to their warmer climates of origin. These findings highlight the complex interplay between domestication, feralization, and current agronomic practices in shaping germination characteristics in Brassica species.

evolutionary biology↗

bioRxiv2023

Warnings/Cautions when collecting Brassica diversity along a large climatic gradient

Agriculture faces great challenges to overcome global warming and to improve system sustainability, requiring access to novel genetic diversity. So far, wild populations and local landraces remain poorly explored. This is notably the case for the two diploid species, Brassica oleracea L. (CC, 2n=2x=18) and B. rapa L. (AA, 2n=2x=20). In order to explore genetic diversity in both species, we have collected numerous populations in their center of origin, the Mediterranean basin, on a large contrasting climatic and soil gradient from northern Europe to southern sub-Saharan regions. In these areas, we also collected 14 populations belonging to five B. oleracea closely related species. Before further genetic and agronomic investigations, we controlled the absence of species misidentification using flow cytometry, sequencing of species specific chloroplast genomic region, as well as cytogenetic analyses in case of unexpected results. Looking at the 102 B. oleracea and 146 B. rapa populations showing a good germination among the 112 and 154 populations collected, seventeen populations were misidentified. The most frequent mistake was a confusion of these diploid species with B. napus. Additionally for B. rapa, 2 autotetraploid populations were observed. Habitats of the collected wild populations and landraces are described in our work. This provides a unique plant material characterization that will pave the way for further analyses investigating the genomic regions involved in climatic and microbiota adaptation. This research is supported by the H2020 Prima project BrasExplor.

ecology↗

bioRxiv2023

Past family selection in Populus nigra leads to an amplification of rust damages when neighbors are related

The competitive ability of domesticated plants, which may have conferred a fitness advantage in the wild, may result in a reduction of yield in agricultural and forestry contexts, as what matters is the group rather than the individual performance. Traits related to competitive ability can be affected by the presence or absence of related individuals in their neighborhood. Consequently, local relatedness might reveal plant-to-plant interaction that can enhance the predictive abilities of genomic models when accounted for, though it remains difficult to measure. To overcome this difficulty, we analyzed data from the French breeding program of Populus nigra L., where 1,452 genotypes were replicated six to eight times, each time encountering a different neighborhood. We assessed local relatedness and investigated genomic estimated breeding values on tree height and vulnerability to rust with a single-step GBLUP incorporating local relatedness as a covariate. The results indicate that incorporating local relatedness as an additional factor in GBLUP models has a significantly greater influence on resistance to rust than on tree height, though its overall effect on genomic predictions themselves was limited. The influence of local relatedness is small but likely trait-specific, and the genetic architecture of the trait under selection could attenuate or improve the efficacy of breeding for group performance.

genetics↗

bioRxiv2022

The role of intraspecific competition during post-glacial recolonization: a Norway spruce case study

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in, and post-glacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density and tracheid traits at breast height. Data from 4,461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly pre-adapted, mainly through growth-related traits.

genetics↗

bioRxiv2022

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones. Significance StatementUnderstanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.

evolutionary biology↗

bioRxiv2021

How to reach a higher selection plateau with optimal contribution selection and compensatory mating?

In breeding, Optimal Contribution Selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic - through coancestry - is undoubtedly the reason for the success of OCS, as it avoids initial loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for Genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multi-generation breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study of Populus nigra, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau.

evolutionary biology↗

bioRxiv2020

Phenotypic plasticity, population structure and adaptation in a young weed species with a worldwide distribution

The colonization success of a species depends on phenotypic plasticity, adaptive potential and population structure. Assessing their relative contributions during a colonization process is challenging, and a large-scale experiment had yet to be done. In this study, we attempted to tease apart their effects on the fitness of one of the most common plant on Earth, the shepherds purse (Capsella bursa-pastoris), a self-fertilizing and allopolyploid weed, with a worldwide distribution. The overarching goal is to eventually understand how the shepherds purse extensive distribution range was established so rapidly. To do so, we carried out three common gardens, located in Europe, Asia and North America, and measured several life-history traits on field-collected accessions belonging to three distinct genetic clusters (Middle East, Europe, and Asia). Our experiment showed that (i) the success of C. bursa-pastoris is mainly due to its high degree of phenotypic plasticity; and (ii), genetic cluster effect reflected a classic pattern observed in core vs marginal populations, with the Middle Eastern cluster (putative core population) outperforming the European and Asian clusters. This study therefore revealed, in a model species, different relative contributions of plasticity and adaptation to fitness, depending on the population and the time since colonization occurred.

evolutionary biology↗