Genome-wide association studies in plants: the missing heritability is in the field

Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context

Adaptive Value of Phenological Traits in Stressful Environments: Predictions Based on Seed Production and Laboratory Natural Selection

Phenological traits often show variation within and among natural populations of annual plants. Nevertheless, the adaptive value of post-anthesis traits is seldom tested. In this study, we estimated the adaptive values of pre- and post-anthesis traits in two stressful environments (water stress and interspecific competition), using the selfing annual species Arabidopsis thaliana. By estimating seed production and by performing laboratory natural selection (LNS), we assessed the strength and nature (directional, disruptive and stabilizing) of selection acting on phenological traits in A. thaliana under the two tested stress conditions, each with four intensities. Both the type of stress and its intensity affected the strength and nature of selection, as did genetic constraints among phenological traits. Under water stress, both experimental approaches demonstrated directional selection for a shorter life cycle, although bolting time imposes a genetic constraint on the length of the interval between bolting and anthesis. Under interspecific competition, results from the two experimental approaches showed discrepancies. Estimation of seed production predicted directional selection toward early pre-anthesis traits and long post-anthesis periods. In contrast, the LNS approach suggested neutrality for all phenological traits. This study opens questions on adaptation in complex natural environment where many selective pressures act simultaneously

Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot

Funding: Strategic Priority Research Program of Chinese Academy of Sciences (XDA 20050203 (H.S.); Major Program of the NSFC 31590823 (H.S.); National Key R & D Program of China 2017YF0505200 (H.S.); NSFC (31670198 to J.C., 31560062 to Y.H.,31871271 to W.Z.); Science and Technology Research Program of KIB (NO.KIB2016005 to J.C.); Youth Innovation Promotion Association, CAS (J.C.), and Peking-Tsinghua Center for Life Science, the State Key Laboratory of Protein and PlantGene Research and Qidong-SLS Innovation Fund (W.Z.).The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.Publisher PDFPeer reviewe

data for "Plant genetic effects on microbial hubs impact host fitness in repeated field trials"

These are data tables required for the analysis of the paper "Plant genetic effects on microbial hubs impact host fitness in repeated field trials". All scripts are available at https://forgemia.inra.fr/bbrachi/microbiota_paper.git The folder architecture in the zip files is the same as in the repository: https://forgemia.inra.fr/bbrachi/microbiota_paper.git The dataset includes: - OTU count tables for 16S and ITS - taxonomic assignation - plant seed-set estimates - plant growth data from the B38 experiment. - Metabolomics dataset

Using ecological genomics to study the natural variation of phenological traits in Arabidopsis thaliana

L’étude de la l’adaptation de traits complexes passe par deux approches complémentaires. La première approche vise à décrire les architectures et les bases génétiques de variation naturelle adaptative. La seconde approche, vise à décrire les échelles géographiques de la variation phénotypique et les facteurs écologiques agissant comme pressions de sélection sur le trait étudié. Ces deux approches sont utilisées pour étudier la variation naturelle de traits phénologiques chez Arabidopsis thaliana.Les architectures et les bases génétiques de la variation naturelle de traits phénologiques, phénotypés dans deux environnements, ont été étudiées en tirant avantage de la combinaison ‘genome-wide association (GWA) mapping’ et cartographie de QTL. Cette combinaison a permis de mettre en évidence que les effets alléliques et l’identité des gènes liés à la variation naturelle étaient fortement dépendants de l’environnement et que les populations naturelles pourraient avoir suivi des marches adaptatives différentes. La caractérisation phénologique, écologique et génétique d’un échantillonnage hiérarchique de populations d’A. thaliana a mis en évidence que la variation des traits phénologiques était adaptative à une échelle très locale en réponse à de nombreux facteurs climatiques et édaphiques. Cette double approche génomique - écologie suggère que l’étude des marches adaptatives des populations naturelles d’A. thaliana vers des optimums phénotypiques doit passer par l’étude des architectures et des bases génétiques à différentes échelles géographiques, suivant un dispositif hiérarchisé et que l’estimation de la variation naturelle doit s’effectuer dans des conditions réalistes.Two complementary approaches need to be considered in the study of adaptation. The first approach aims at describing the genetic architectures and the genetic bases of phenotypic variation in order to better understand the adaptive walk followed by natural populations toward a phenotypic optimum. The second approach aims to identify the environmental grain of the ecological factors acting as selective pressures in natural populations. In this work we studied the natural variation of phenological traits in Arabidopsis thaliana. We used a powerful combination of genome wide association (GWA) mapping and traditional QTL mapping to fine map the genetics of phenological traits measured under two environments. This dual mapping strategy revealed a strong environmental dependency of both allelic effect and identity of the genes underlying natural variation, but also that natural A. thaliana populations may have followed different adaptive walks. A. thaliana populations were sampled according a hierarchical geographic pattern and characterized ecologically, phenologically and genetically. This strategy revealed that phenological traits were adaptive to fine-grained environmental conditions defined by both climate and soil conditions. In the study of the adaptive walks followed by A. thaliana natural populations, this two sided approach, combining both genomics and ecology, suggests that the description of the genetic architectures and the identification of causal genes should be performed at different spatial scales, following a hierarchical geographic design, and that phenotypes must be measured in ecologically realistic conditions

Étude de la variation naturelle de traits phénologiques chez Arabidopsis thaliana par une approche de génomique écologique

L étude de la l adaptation de traits complexes passe par deux approches complémentaires. La première approche vise à décrire les architectures et les bases génétiques de variation naturelle adaptative. La seconde approche, vise à décrire les échelles géographiques de la variation phénotypique et les facteurs écologiques agissant comme pressions de sélection sur le trait étudié. Ces deux approches sont utilisées pour étudier la variation naturelle de traits phénologiques chez Arabidopsis thaliana.Les architectures et les bases génétiques de la variation naturelle de traits phénologiques, phénotypés dans deux environnements, ont été étudiées en tirant avantage de la combinaison genome-wide association (GWA) mapping et cartographie de QTL. Cette combinaison a permis de mettre en évidence que les effets alléliques et l identité des gènes liés à la variation naturelle étaient fortement dépendants de l environnementet que les populations naturelles pourraient avoir suivi des marches adaptatives différentes. La caractérisation phénologique, écologique et génétique d un échantillonnage hiérarchique de populations d A. thaliana a mis en évidence que la variation des traits phénologiques était adaptative à une échelle très locale en réponse à de nombreux facteurs climatiques et édaphiques. Cette double approche génomique - écologie suggère que l étude des marches adaptatives des populations naturelles d A. thaliana vers des optimums phénotypiques doit passer par l étude des architectures et des bases génétiques à différentes échelles géographiques, suivant un dispositif hiérarchiséet que l estimation de la variation naturelle doit s effectuer dans des conditions réalistes.Two complementary approaches need to be considered in the study of adaptation. The first approach aims at describing the genetic architectures and the genetic bases of phenotypic variation in order to better understand the adaptive walk followed by natural populations toward a phenotypic optimum. The second approach aims to identify the environmental grain of the ecological factors acting as selective pressures in natural populations. In this work we studied the natural variation of phenological traits in Arabidopsis thaliana. We used a powerful combination of genome wide association (GWA) mapping and traditional QTL mapping to fine map the genetics of phenological traits measured under two environments. This dual mapping strategy revealed a strong environmental dependency of both allelic effect and identity of the genes underlying natural variation, but also that natural A. thaliana populations may have followed different adaptive walks. A. thaliana populations were sampled according a hierarchical geographic pattern and characterized ecologically, phenologically and genetically. This strategy revealed that phenological traits were adaptive to fine-grained environmental conditions defined by both climate and soil conditions. In the study of the adaptive walks followed by A. thaliana natural populations, this two sided approach, combining both genomics and ecology, suggests that the description of the genetic architectures and the identification of causal genes should be performed at different spatial scales, following a hierarchical geographic design, and that phenotypes must be measured in ecologically realistic conditions.LILLE1-Bib. Electronique (590099901) / SudocSudocFranceF

Gender variation and inbreeding depression in gynodioecious-gynomonoeicous Silene nutans (Caryophyllaceae)

International audienceGynodioecy involves the stable co-occurrence of females and hermaphrodites. Its maintenance theoretically depends on differences in female and male reproductive success among gender morphs. Although many gynodioecious species also include gynomonoecious individuals that carry a mixture of female and perfect flowers, little is known about the male and female fitness of this third morph. Here, we present the first study of the reproductive system of Silene nutans, including females, gynomonoecious plants, and hermaphrodites. By measuring 10 floral traits in controlled conditions, we showed that females bear smaller and lighter flowers than hermaphrodites, with female and perfect flowers of gynomonoecious plants being intermediates. By measuring pollen quantity and quality, we showed that gynomonoecious plants had a lower potential male fitness than hermaphrodites at the level of both flowers and individuals. In addition, gynomonoecious plants were shown to widely vary their proportion of female flowers (0.03–0.9) and their floral traits, suggesting a quantitative restoration of male fertility. Finally, controlled pollinations showed evidence for inbreeding depression (d ¼ 0:3) in progeny of hermaphrodites and gynomonoecious individuals, affecting both pre- and postdispersal traits; this could provide a selective advantage for females

Gender variation and inbreeding depression in gynodioecious‐gynomonoecious silene nutans (Caryophyllaceae)

International audienceGynodioecy involves the stable co‐occurrence of females and hermaphrodites. Its maintenance theoretically depends on differences in female and male reproductive success among gender morphs. Although many gynodioecious species also include gynomonoecious individuals that carry a mixture of female and perfect flowers, little is known about the male and female fitness of this third morph. Here, we present the first study of the reproductive system of Silene nutans, including females, gynomonoecious plants, and hermaphrodites. By measuring 10 floral traits in controlled conditions, we showed that females bear smaller and lighter flowers than hermaphrodites, with female and perfect flowers of gynomonoecious plants being intermediates. By measuring pollen quantity and quality, we showed that gynomonoecious plants had a lower potential male fitness than hermaphrodites at the level of both flowers and individuals. In addition, gynomonoecious plants were shown to widely vary their proportion of female flowers (0.03–0.9) and their floral traits, suggesting a quantitative restoration of male fertility. Finally, controlled pollinations showed evidence for inbreeding depression ( ) in progeny of hermaphrodites and gynomonoecious individuals, affecting both pre‐ and postdispersal traits; this could provide a selective advantage for females