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Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives
No full textCustom R and bash codes used for the analyses are available on https://github.com/sylvainglemin/ms-rec-triticeae along with input files. Software for genotype calling (reads2snps v. 2.0.64, ORF_extractor.pl) and polymorphism estimates (dNdSpNpS v.3) are available at https://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools. Morphological trait measures are provided in Supplementary Tables S2 and S3.Filtered and cleaned sequence alignments to perform polymorphism analyses are available at https://bioweb.supagro.inra.fr/WheatRelativeHistory/index.php?menu=downloadMating. Raw data are deposited at the Sequence Read Archives (SRA) under project PRJNA945064 (submission number SUB12943046).International audienceHow and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome-wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops/Triticum grass species, a group characterized by contrasted mating systems (from obligate outcrossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome-wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and, more generally, for our understanding of the fundamental drivers of genetic diversity
Light pollution, a complex real-world problem to be tackled through an interdisciplinary approach
No full textInternational audienceThe problems of light pollution and the unprecedented issues raised by its management in the many territories currently concerned with the preservation of the nocturnal environment are complex real-world problems. This complexity and the need to grasp these issues in their entirety are now forcing researchers to go beyond traditional disciplinary approaches to truly interdisciplinary studies at the interface between the sciences of the Universe, the environmental sciences and the social sciences. In order to organize this production of interdisciplinary knowledge and encourage its transfer to territorial action, the French National Center for Scientific Research (CNRS) has created in 2021 the Nocturnal Environment Observatory (NEO — https://observatoire-environnement-nocturne.cnrs.fr/en/). Through its research programs, actions and partnerships with various territories, the Nocturnal Environment Observatory brings together a large community of scientists from different disciplines and institutions (social and natural sciences, sciences of the Universe, engineering and environmental physics), experts from different and complementary professional fields, as well as agents at the service of protected area management structures and territorial projects. Through the case study of Reunion island — a densely inhabited area under severe ecological constraints — we will present the objectives, the analytical framework, the tools and the methods of the NEO. We will show the concrete contributions to territorial action of a radically interdisciplinary research on the nocturnal environment, a socio-ecosystemic object built on the foundations of the Dark-sky movement, and therefore owes much to the work of the astronomical community since the second half of the 20th century
Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping
No full textThe genotypic and phenotypic data are available here https://doi.org/10.18167/DVN1/TZVGLS. The scripts to reproduce the results are available here https://gitlab.cirad.fr/agap/giv/sorghum_bcnam_analysis. The results were gathered into an interactive database available here https://github.com/vincentgarin/SQE. For plant material, please contact the corresponding authors for availability.International audienceIdentifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties
Efficiency of simple sequence repeat (SSR) markers in genetic diversity study and differentiation of Borassus aethiopum Mart. and Borassus akeassii Bayton, Ouédr. and Guinko
No full textInternational audienceThe African fan palm, Borassus aethiopum, is widely distributed in West and Central Africa. To contribute to the understanding of its evolutionary history and geographical distribution, we have performed the analysis of its genetic diversity and population structure through a wide samples collection in different countries. Simple sequences repeat (SSR) markers were used to assess the population structure and genetic diversity of such samples. Genetic diversity was estimated for a total of 201 samples of B. aethiopum using 13 SSR markers. The result of our analysed populations indicated a mean value of expected heterozygosity (He) of 0.395, suggesting a moderate genetic diversity, with 62% and 37% of molecular variance within individuals and among populations, respectively. Clustering analysis by using Bayesian method and principal component analysis clustered populations into two main groups corresponding to the two sampling regions (West and Central Africa), and each group consists of two genetic clusters. In addition to this, we tested the ability of the same SSR markers to discriminate between both fan palm species occurring in sub-Saharan Africa, namely B. aethiopum and B. akeassii. Hence, our markers can be used as molecular tools for differentiating both species and furthermore for genetic diversity of B. akeassii populations
A Multivalued, Spatialized, and Timed Modelling Language for Social-Ecological Systems
No full textInternational audienceThe eden framework provides tools for the formal modelling and analysis of social-ecological systems and their dynamics. In particular, it features the rr modelling language (for reaction rules) that allows defining systems as Boolean variables and guarded actions to update them. This language is equipped with a compact semantics in terms of Petri nets extended with read-arcs, inhibitor arcs, reset arcs, and transition priorities. Apart from the last one, these extensions can be implemented in standard Petri nets at the price of building bigger nets. In this paper, we extend the rr language with multivalued variables, spatial information inspired by membrane computing, and timing. The resulting language, called mrr (for multivalued rr), is equipped with a compact colored Petri nets semantics extended with only transition priorities. © 2024 Copyright for this paper by its authors
Extra‐pair paternity in two passerine birds breeding in a gradient of urbanisation
No full textInternational audienceUrbanisation has been increasing worldwide in recent decades, driving environmental change and exerting novel selective pressures on wildlife. Phenotypic differences between urban and rural individuals have been widely documented in several taxa. However, the extent to which urbanisation impacts mating strategies is less known. Here, we investigated extra‐pair paternity variation in great tits ( Parus major ) and blue tits ( Cyanistes caeruleus ) breeding in nestboxes set in a gradient of urbanisation in Warsaw, Poland, over three breeding seasons. Urbanisation was quantified as the amount of light pollution, noise pollution, impervious surface area (ISA) and tree cover within a 100‐m radius around each nestbox. We obtained genotypes for 1213 great tits at 7344 SNP markers and for 1299 blue tits at 9366 SNP markers with a genotyping‐by‐sequencing method, and inferred extra‐pair paternity by computing a genomewide relatedness matrix. We report higher extra‐pair paternity in blue tits breeding in more urbanised areas, for example, with higher light pollution and ISA, and lower tree cover. However, no such trend was found in great tits. Late‐stage survival of individual nestlings in both species was not associated with paternity or urbanisation proxies, thus we were not able to detect fitness benefits or drawbacks of being an extra‐pair offspring in relation to urbanisation. Our results contribute to the growing body of knowledge reporting on the effects of urbanisation on avian ecology and behaviour, and confirm species‐specific and population‐specific patterns of extra‐pair paternity variation
L’évaluation des risques pour la santé humaine et celle des sols
No full textNational audiencePour agir de façon rationnelle face à une contamination avérée ou suspectée d’un sol, il est en premier lieu nécessaire d’évaluer les risques toxicologiques (pour la santé humaine) et écotoxicologiques (pour la santé du sol). La communauté scientifique a élaboré une démarche d’évaluation des risques, dont les principes ont d’ailleurs été retenus par l’Union européenne dans sa très récente proposition de directive sur la surveillance et la résilience des sols (la Soil Monitoring Law) [1]. Dans cet article, nous parlons des sols en général et précisons quand il est spécifiquement question des sols agricoles
Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species
No full textUnderstanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters
Identification of a sugarcane bacilliform virus promoter that is activated by drought stress in plants
No full textInternational audienceSugarcane (Saccharum spp.) is an important sugar and biofuel crop in the world. It is frequently subjected to drought stress, thus causing considerable economic losses. Transgenic technology is an effective breeding approach to improve sugarcane tolerance to drought using drought-inducible promoter(s) to activate drought-resistance gene(s). In this study, six different promoters were cloned from sugarcane bacilliform virus (SCBV) genotypes exhibiting high genetic diversity. In beta-glucuronidase (GUS) assays, expression of one of these promoters (PSCBV-YZ2060) is similar to the one driven by the CaMV 35S promoter and >90% higher compared to the other cloned promoters and Ubi1. Three SCBV promoters (PSCBV-YZ2060, PSCBV-TX, and PSCBV-CHN2) function as drought-induced promoters in transgenic Arabidopsis plants. In Arabidopsis, GUS activity driven by promoter PSCBV-YZ2060 is also upregulated by abscisic acid (ABA) and is 2.2-5.5-fold higher when compared to the same activity of two plant native promoters (PScRD29A from sugarcane and PAtRD29A from Arabidopsis). Mutation analysis revealed that a putative promoter region 1 (PPR1) and two ABA response elements (ABREs) are required in promoter PSCBV-YZ2060 to confer drought stress response and ABA induction. Yeast one-hybrid and electrophoretic mobility shift assays uncovered that transcription factors ScbZIP72 from sugarcane and AREB1 from Arabidopsis bind with two ABREs of promoter PSCBV-YZ2060. After ABA treatment or drought stress, the expression levels of endogenous ScbZIP72 and heterologous GUS are significantly increased in PSCBV-YZ2060:GUS transgenic sugarcane plants. Consequently, promoter PSCBV-YZ2060 is a possible alternative promoter for genetic engineering of drought-resistant transgenic crops such as sugarcane
Identification of genetic bases of male fertility in <i>Pyricularia oryzae</i> by Genome Wide Association Study (GWAS)
No full textThe reproductive system of an organism impacts the emergence and evolution of adaptive variants in response to selective constraints. The understanding of the sexual mode of reproduction in pathogens helps to understand their life history. In filamentous Ascomycete fungi, mating type system and the production of gametes are required to reproduce sexually. In the phytopathogenic Ascomycete Pyricularia oryzae , studies of the genetic determinants of sexual reproduction are still limited to the mating type system. This study focuses on identifying the genes involved in male fertility through the production of male gametes known as microconidia. We performed a GWAS analysis coupled with a local score approach on a wild recombinant population of Pyricularia oryzae phenotyped for microconidia production. We identified one genomic region significantly associated with the quantity of microconidia produced. This region contained nine candidate genes, some of them annotated with functions associated to sexual reproduction in model fungi such as Neurospora crassa , Podospora anserina and Sordaria macrospora . The most promising candidate gene contains a Jumonji domain. Proteins belonging to the Jumonji family are conserved among Eukaryotes and are known to be involved in chromatin regulation