High Genetic Diversity and Structure of Colletotrichum gloeosporioides s.l. in the Archipelago of Lesser Antilles.

Colletotrichum gloeosporioides is a species complex of agricultural importance as it causes anthracnose disease on many crop species worldwide, and strong impact regionally on Water Yam (Dioscorea alata) in the Caribbean. In this study, we conducted a genetic analysis of the fungi complex in three islands of the Lesser Antilles-Guadeloupe (Basse Terre, Grande Terre and Marie Galante), Martinique and Barbados. We specifically sampled yam fields and assessed the genetic diversity of strains with four microsatellite markers. We found a very high genetic diversity of all strains on each island, and intermediate to strong levels of genetic structure between islands. Migration rates were quite diverse either within (local dispersal) or between islands (long-distance dispersal), suggesting important roles of vegetation and climate as local barriers, and winds as an important factor in long-distance migration. Three distinct genetic clusters highlighted different species entities, though there was also evidence of frequent intermediates between two clusters, suggesting recurrent recombination between putative species. Together, these results demonstrated asymmetries in gene flow both between islands and clusters, and suggested the need for new approaches to anthracnose disease risk control at a regional level.

Natural Flora Is Indiscriminately Hosting High Loads of Generalist Fungal Pathogen Colletotrichum gloeosporioides Complex over Forest Niches, Vegetation Strata and Elevation Gradient.

Crop pathogenic fungi may originate from reservoir pools including wild vegetation surrounding fields, and it is thus important to characterize any potential source of pathogens. We therefore investigated natural vegetation's potential for hosting a widespread pathogenic group, Colletotrichum gloeosporioides species complex. We stratified sampling in different forest environments and natural vegetation strata to determine whether the fungi were found preferentially in specific niches and areas. We found that the fungi complex was fairly broadly distributed in the wild flora, with high prevalence in every study environment and stratum. Some significant variation in prevalence nevertheless occurred and was possibly associated with fungal growth conditions (more humid areas had greater prevalence levels while drier places had slightly lower presence). Results also highlighted potential differences in disease effects of strains between strata components of study flora, suggesting that while natural vegetation is a highly probable source of inoculums for local crops nearby, differences in aggressiveness between vegetation strata might also lead to differential impact on cultivated crops.

Dynamics of Pathogenic Fungi in Field Hedges: Vegetation Cover Is Differentially Impacted by Weather.

Landscape effects might impede or increase spore dispersal and disease risk for crops, as trees and hedges buffer winds and can behave as spore traps, therefore limiting diffusion of fungi, or, on the contrary, behave as disease relay once vegetation is infected and become inoculum sources. In this study, we investigated weekly prevalence of the pathogenic fungus Colletotrichum gloeosporioides on guava tree leaves, differentiating impacts of leaf height on tree, age, and location within leaf. We first estimated differences in prevalence for each covariate, and then related infection rates to weather effects during the year. Our results highlighted a great variance of prevalence among individual trees, and a lower contamination of tree tops, as well as a tendency for greater odds of infection in tips of young leaves compared to older ones. Last, we show evidence that individual tree contaminations are associated with different disease dynamics: early and dispersal-based, late and growth-based, as well as with intermediate dynamic ranges. Pathogen infection dynamics will thus be greatly impacted by cover characteristics at local scale, and tree cover should not be perceived as homogeneously driving disease levels.

Weeds as Pathogen Hosts and Disease Risk for Crops in the Wake of a Reduced Use of Herbicides: Evidence from Yam (Dioscorea alata) Fields and Colletotrichum Pathogens in the Tropics.

The transition toward sustainable agriculture requires rethinking cropping systems in the light of less intensive and chemically reliant practices. Weed management is one of the target practices to evolve cropping systems with decreased impact on the environment. While softened management will lead to increased weeds/crops coexistence, it is of importance to assess the relative benefits and drawbacks of new practices. Among the potential drawbacks of weeds/crops coexistence, disease risk may increase if weeds are hosting pathogens. In this study, we assessed the potential of weeds for hosting pathogenic generalist fungi known to translate into disease in crops. We first describe prevalence in fields after harvest and relate prevalence to species characteristics and communities. Then, we directly test the idea that weeds serve as inoculums sources during cropping with a natural experiment. This study highlights variation in host skill among feral weeds for Colletotrichum species, including potential congeneric sub-specialization on different weeds within communities. Last, prevalence within fields was more correlated to focal crop inoculation rates compared to local weed load, but there was a significant correlation effect with prevalence on weeds in the vicinity of fields, suggesting that weeds are mediating disease levels at the local scale, too. Results pointed to the importance of weed host skill in disease risk yet open the door to the potential control of pathogens via targeted weed management.

Data on microsatellite markers in Colletotrichum gloeosporioides s.l., polymorphism levels and diversity range.

Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2-29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.

Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers.

Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods.

Varietal Dynamics and Yam Agro-Diversity Demonstrate Complex Trajectories Intersecting Farmers' Strategies, Networks, and Disease Experience.

Loss of varietal diversity is a worldwide challenge to crop species at risk for genetic erosion, while the loss of biological resources may hinder future breeding objectives. Loss of varieties has been mostly investigated in traditional agricultural systems where variety numbers are dramatically high, or for most economically important crop species for which comparison between pre-intensive and modern agriculture was possible. Varietal dynamics, i.e., turnover, or gains and losses of varieties by farmers, is nevertheless more rarely studied and while we currently have good estimates of genetic or varietal diversity for most crop species, we have less information as to how on farm agro-diversity changes and what cause its dynamics. We therefore investigated varietal dynamics in the agricultural yam system in the Caribbean island of Guadeloupe. We interviewed producers about varieties they cultivated in the past compared to their current varieties, in addition to characterizing yam cropping characteristics and both farm level and producers socio-economic features. We then used regression tree analyses to investigate the components of yam agro-diversity, varietal dynamics and impact of anthracnose on varieties. Our data demonstrated that no dramatic loss of varieties occurred within the last decades. Cultivation changes mostly affected widespread cultivars while frequency of uncommon varieties stayed relatively stable. Varietal dynamics nevertheless followed sub-regional patterns, and socio-economic influences such as producer age or farm crop diversity. Recurrent anthracnose epidemics since the 1970s did not alter varietal dynamics strongly, but sometimes translated into transition from Dioscorea alata to less susceptible species or into a decrease of yam cultivation. Factors affecting changes in agro-diversity were not relating to agronomy in our study, and surprisingly there were different processes delineating short term from long term varietal dynamics, independently of disease risk. Our results highlighted the importance of understanding varietal dynamics, an often overlooked component of agriculture sustainability, in addition to evolutionary forces shaping agro-diversity and genetic diversity distribution within crops. It is also crucial to understand how processes involved do scale up worldwide and for different crop species, so as not to mislead on-farm conservation efforts and efficacy of agro-diversity preservation.

Direct splash dispersal prevails over indirect and subsequent spread during rains in Colletotrichum gloeosporioides infecting yams.

Plant pathogens have evolved many dispersal mechanisms, using biotic or abiotic vectors or a combination of the two. Rain splash dispersal is known from a variety of fungi, and can be an efficient driver of crop epidemics, with infectious strains propagating rapidly among often genetically homogenous neighboring plants. Splashing is nevertheless a local dispersal process and spores taking the droplet ride seldom move farther than a few decimeters. In this study, we assessed rain splash dispersal of conidia of the yam anthracnose agent, Colletotrichum gloeosporioides, in an experimental setting using a rain simulator, with emphasis on the impact of soil contamination (i.e., effect of re-splashing events). Spores dispersed up to 50 cm from yam leaf inoculum sources, though with an exponential decrease with increasing distance. While few spores were dispersed via re-splash from spore-contaminated soil, the proportion deposited via this mechanism increased with increasing distance from the initial source. We found no soil contamination carryover from previous rains, suggesting that contamination via re-splashing from contaminated soils mainly occurred within single rains. We conclude that most dispersal occurs from direct splashing, with a weaker contribution of indirect dispersal via re-splash.

Early inbreeding depression in the sexually polymorphic plant Dianthus sylvestris (Caryophyllaceae): Effects of selfing and biparental inbreeding among sex morphs.

Predominantly outcrossing plant species are expected to accumulate recessive deleterious mutations, which can be purged when in a homozygous state following selfing. Individuals may vary in their genetic load because of different selfing histories, which could lead to differences in inbreeding depression among families. Lineage-dependent inbreeding depression can appear in gynodioecious species if obligatory outcrossed females are more likely to produce female offspring and if partially selfing hermaphrodites are more likely to produce hermaphrodites. We investigated inbreeding depression at the zygote, seed, and germination stages in the gynomonoecious-gynodioecious Dianthus sylvestris, including pure-sexed plants and a mixed morph. We performed hand-pollinations on 56 plants, belonging to the three morphs, each receiving 2-3 cross treatments (out-, sib- and self-pollination) on multiple flowers. Effects of cross treatments varied among stages and influenced seed provisioning, with sibling competition mainly occurring within outcrossed fruits. We found significant inbreeding depression for seed mass and germination and cumulative early inbreeding depression varied greatly among families. Among sex morphs, we found that females and hermaphrodites differed in biparental inbreeding depression, whereas uniparental was similar for all. Significant inbreeding depression levels may play a role in female maintenance in this species, and individual variation in association with sex-lineages proclivity is discussed.

Phylogenetic comparative analysis of microsporogenesis in angiosperms with a focus on monocots.

This paper presents the first broad overview of three main features of microsporogenesis (male meiosis) in angiosperms: cytokinesis (cell division), intersporal wall formation, and tetrad form. A phylogenetic comparative approach was used to test for correlated evolution among these characters and to make hypotheses about evolutionary trends in microsporogenesis. The link between features of microsporogenesis and pollen aperture type was examined. We show that the pathway associated with successive cytokinesis (cytoplasm is partitioned after each meiotic division) is restricted to wall formation mediated by centrifugally developing cell plates, and tetragonal (or decussate, T-shaped, linear) tetrads. Conversely, much more flexibility is observed when cytokinesis is simultaneous (two meiotic divisions completed before cytoplasmic partitioning). We suggest that the ancestral type of microsporogenesis for angiosperms, and perhaps for all seed plants, associated simultaneous cytokinesis with centripetal wall formation, resulting in a large diversity in tetrad forms, ranging from regular tetrahedral to tetragonal tetrads, including rhomboidal tetrads. From this ancestral pathway, switches toward successive cytokinesis occurred among basal angiosperms and monocots, generally associated with a switch toward centrifugal intersporal wall formation, whereas eudicots evolved toward an almost exclusive production of regular tetrahedral tetrads. No straightforward link is found between the type of microsporogenesis and pollen aperture type.

Constraints and selection: insights from microsporogenesis in Asparagales.

Developmental constraints have been proposed to interfere with natural selection in limiting the available set of potential adaptations. Whereas this concept has long been debated on theoretical grounds, it has been investigated empirically only in a few studies. In this article, we evaluate the importance of developmental constraints during microsporogenesis (male meiosis in plants), with an emphasis on phylogenetic patterns in Asparagales. Different developmental constraints were tested by character reshuffling or by simulated distributions. Among the different characteristics of microsporogenesis, only cell wall formation appeared as constrained. We show that constraints may also result from biases in the correlated occurrence of developmental steps (e.g., lack of successive cytokinesis when wall formation is centripetal). We document such biases and their potential outcomes, notably the establishment of intermediate stages, which allow development to bypass such constraints. These insights are discussed with regard to potential selection on pollen morphology.

Direct and indirect effects of a sex-biased antagonist on male and female fertility: consequences for reproductive trait evolution in a gender-dimorphic plant.

Gender-dimorphic plants are often subject to sex-differential enemy attack, but whether and how this contributes to trait evolution is unknown. To address this gap, we documented the spatiotemporal prevalence of sex-biased weevil damage in a gynodioecious strawberry. We then conducted path analysis to evaluate the direct and indirect pathways for weevils to affect female and male fertility and to mediate selection in two experimental gardens. Direct effects of weevils significantly reduced fertility and mediated selection on reproductive traits, even in the nonpreferred sex (females). Weevils significantly reduced floral display size in hermaphrodites in both gardens, and this translated into a substantial negative indirect effect on male fertility in the garden where the pathway to fertility via display was stronger. Thus, indirect effects of weevils can contribute to selection in hermaphrodites, which gain the majority of their fitness via male function. Our results also indicate that weevils often play a larger role than pollinators in shaping reproductive phenotype and thus raise the intriguing possibility that antagonists may be drivers of sexual dimorphism. Finally, our results support the view that mutualists, antagonists, and the abiotic environment should be considered when attempting to understand reproductive trait evolution in gender-dimorphic species.