New microsatellite markers for Dacryodes edulis (Burseraceae), an indigenous fruit tree species from Central Africa

Microsatellites were designed and characterized in the African fruit tree species Dacryodes edulis (Burseraceae). The fruits are commercialized throughout Central Africa and the species is present in forested environments as well as cultivated systems. The high variability of these markers makes them suitable to investigate the structure of genetic diversity in this important food tree species from Central Africa. From a genomic library obtained by next-generation sequencing, 21 new polymorphic microsatellite loci were developed. Tested on 95 individuals from four populations coming from three countries of the Congo Basin, the microsatellites displayed two to 20 alleles (mean 7.5; expected heterozygosity 0.003 to 0.937, mean 0.666). The transferability of microsatellites was effective for four other Dacryodes species (D. buettneri, D. igaganga, D. osika, D. pubescens). This set of newly developed microsatellite markers will be useful for assessing the genetic diversity and differentiation as well as gene flow patterns of D. edulis in tropical forests from Central Africa

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping

Microsatellite markers development for Indonesian nutmeg (Myristica fragrans Houtt.) and transferability to other Myristicaceae spp

Myristica fragrans (Myristicaceae) is a tropical evergreen tree that yields the two famous spices: nutmeg and mace. Despite its socio-economic importance, the spatial distribution of its genetic diversity is barely documented. In this aim, 48 nuclear microsatellite markers were isolated of which 14 were polymorphic in M. fragrans. Number of alleles per locus ranged from 2 to 6. The level of observed heterozygosity ranged from 0.038 to 0.929 across loci. Transferability of these microsatellites in other Myristica species (M. fatua, M. argentea, and M. crassipes) and Myristicaceae species (Horsfieldia palauensis) was tested and successful. These new microsatellites will be useful for future investigation on genetic diversity and population structure of M. fragrans and phylogenetically-related species

Data from: Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin

Local people's perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd (Crescentia cujete), whose versatile fruits have technological, symbolic and medicinal uses. A wild relative (C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the proportions of admixture correlate with fruit size variation of cultivated trees. New morphotypes arise from hybridization, and are recognized by people and named as local varieties. Small hybrid fruits are used to make the important symbolic rattle (maracá), suggesting that management of hybrid trees is an ancient human practice in Amazonia. Effective conservation of Amazonian agrobiodiversity needs to incorporate this interaction between wild and cultivated populations that is managed by smallholder families. Beyond treegourd, our study clearly shows that hybridization plays an important role in tree crop phenotypic diversification, and that the integration of molecular analyses and farmers'perceptions of diversity help disentangle crop domestication history

Sterile inflammation of endothelial cell-derived apoptotic bodies is mediated by interleukin-1α

Sterile inflammation resulting from cell death is due to the release of cell contents normally inactive and sequestered within the cell; fragments of cell membranes from dying cells also contribute to sterile inflammation. Endothelial cells undergoing stress-induced apoptosis release membrane microparticles, which become vehicles for proinflammatory signals. Here, we show that stress-activated endothelial cells release two distinct populations of particles: One population consists of membrane microparticles (<1 μm, annexin V positive without DNA and no histones) and another larger (1–3 μm) apoptotic body-like particles containing nuclear fragments and histones, representing apoptotic bodies. Contrary to present concepts, endothelial microparticles do not contain IL-1α and do not induce neutrophilic chemokines in vitro. In contrast, the large apoptotic bodies contain the full-length IL-1α precursor and the processed mature form. In vitro, these apoptotic bodies induce monocyte chemotactic protein-1 and IL-8 chemokine secretion in an IL-1α–dependent but IL-1β–independent fashion. Injection of these apoptotic bodies into the peritoneal cavity of mice induces elevated serum neutrophil-inducing chemokines, which was prevented by cotreatment with the IL-1 receptor antagonist. Consistently, injection of these large apoptotic bodies into the peritoneal cavity induced a neutrophilic infiltration that was prevented by IL-1 blockade. Although apoptosis is ordinarily considered noninflammatory, these data demonstrate that nonphagocytosed endothelial apoptotic bodies are inflammatory, providing a vehicle for IL-1α and, therefore, constitute a unique mechanism for sterile inflammation

Structure of sweet potato (Ipomoea batatas) diversity in West Africa covaries with a climatic gradient.

Sub-Saharan agriculture has been identified as vulnerable to ongoing climate change. Adaptation of agriculture has been suggested as a way to maintain productivity. Better knowledge of intra-specific diversity of varieties is prerequisites for the successful management of such adaptation. Among crops, root and tubers play important roles in food security and economic growth for the most vulnerable populations in Africa. Here, we focus on the sweet potato. The Sweet potato (Ipomoea batatas) was domesticated in Central and South America and was later introduced into Africa and is now cultivated throughout tropical Africa. We evaluated its diversity in West Africa by sampling a region extending from the coastal area of Togo to the northern Sahelian region of Senegal that represents a range of climatic conditions. Using 12 microsatellite markers, we evaluated 132 varieties along this gradient. Phenotypic data from field trials conducted in three seasons was also obtained. Genetic diversity in West Africa was found to be 18% lower than in America. Genetic diversity in West Africa is structured into five groups, with some groups found in very specific climatic areas, e.g. under a tropical humid climate, or under a Sahelian climate. We also observed genetic groups that occur in a wider range of climates. The genetic groups were also associated with morphological differentiation, mainly the shape of the leaves and the color of the stem or root. This particular structure of diversity along a climatic gradient with association to phenotypic variability can be used for conservation strategies. If such structure is proved to be associated with specific climatic adaptation, it will also allow developing strategies to adapt agriculture to ongoing climate variation in West Africa

Diversity of Treegourd (Crescentia cujete) Suggests Introduction and Prehistoric Dispersal Routes into Amazonia

The use and dispersal of domesticated plants may reflect patterns of early human diffusion of technologies and lifestyles. Treegourd (Crescentia cujete) has fruits with ancient utilitarian and symbolic value in the Neotropics. We assessed diversity based on chloroplast (SNPs), nuclear (SSR) markers, and fruit shapes of cultivated treegourds and wild relatives across Amazonia and Mesoamerica in order to discuss hypothesis of dispersal routes and diversification of fruits along its distribution. The haplotype network showed three distinct groups: Crescentia amazonica, wild Mesoamerican C. cujete, and cultivated C. cujete from Brazilian Amazonia and Mexico. Mexico and Brazil shared two haplotypes, with slightly different distributions in Amazonia. The most divergent haplotype is well-represented in Eastern Amazonia. Nuclear differentiation between Mesoamerican wild and cultivated C. cujete is relatively low (FST = 0.35), compared with Amazonian cultivated (FST = 0.45–0.61). Differentiation is also higher between wild C. amazonica and cultivated C. cujete (FST = 0.57), but modest within cultivated C. cujete from Amazonia and Mexico (FST = 0.04), with higher genetic similarity in northwestern Amazonia. Mexico and Amazonia showed similar chloroplast nucleotide diversity (4.66 × 10−2 and 5.31 × 10−2, respectively), although sample sizes are very different. Except in Northwestern and Eastern Amazonia, we found ample genetic homogeneity of cultivated C. cujete across Amazonia, but highest morphological diversity in the Northwest, with fruit shapes that are absent in Mexico. We conclude that treegourds introduced into the Amazon Basin and Mexico share a common ancestry with a currently unknown origin. The patterns of genetic diversity across Amazonia allow two hypotheses of the routes of introduction: a northwestern introduction into the Negro and Solimões Rivers, and an eastern introduction from the coastal Guianas into the Amazonas River. The dispersal into Amazonia followed previously proposed routes of human and plant migrations. The contrasting fruit shape diversity suggests different utilitarian demands and cultural preferences for treegourd fruits between Mexico and Amazonia

Sequence_alignments_cp_treegourd

The sequence alignments are shown using the nexus format. This file was applied to estimate chloroplast diversity analysis and construct the haplotype network, performed respectively in DNAsp and POPART softwares. The labels of the samples correspond to the Sequencing_codes in the passport (Table S1)

Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

International audienceBackground: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results: During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) an