Targeted capture of Dreb subfamily genes as candidates genes for drought tolerance polymorphism in natural population of Coffea canephora.

Coffea canephora, (Robusta), provides 33% of worldwide coffee production, 80% and 22% of Ugandan and Brazilian coffee production, respectively. Abiotic stress such as temperature variations or drought periods, aggravated by climate changes, are factors that affect this production. This sensitivity threatens both the steady supply of quality coffees and the livelihood of millions of people producing coffee. The natural genetic diversity of C. canephora offer a potential for detecting new genetic variants related to drought adaptation. In particular, modifications occurring in genes related to abiotic stress tolerance make these genes candidate for breeding programs in order to enhance the resilience to climate change

Spatial and Temporal Variation in Selection of Genes Associated with Pearl Millet Varietal Quantitative Traits In situ

Ongoing global climate changes imply new challenges for agriculture. Whether plants and crops can adapt to such rapid changes is still a widely debated question. We previously showed adaptation in the form of earlier flowering in pearl millet at the scale of a whole country over three decades. However, this analysis did not deal with variability of year to year selection. To understand and possibly manage plant and crop adaptation, we need more knowledge of how selection acts in situ. Is selection gradual, abrupt, and does it vary in space and over time? In the present study, we tracked the evolution of allele frequency in two genes associated with pearl millet phenotypic variation in situ. We sampled 17 populations of cultivated pearl millet over a period of 2 years. We tracked changes in allele frequencies in these populations by genotyping more than seven thousand individuals. We demonstrate that several allele frequencies changes are compatible with selection, by correcting allele frequency changes associated with genetic drift. We found marked variation in allele frequencies from year to year, suggesting a variable selection effect in space and over time. We estimated the strength of selection associated with variations in allele frequency. Our results suggest that the polymorphism maintained at the genes we studied is partially explained by the spatial and temporal variability of selection. In response to environmental changes, traditional pearl millet varieties could rapidly adapt thanks to this available functional variability

Modelling dependency networks to inform data structures in BIM and smart cities

The pervasive deployment of "smart city" and "smart building" projects in cities world-wide is driving innovation on many fronts including; technology, telematics, engineering and entrepreneurship. This paper focuses on the technical and engineering perspectives of BIM and smart cities, by extending building and urban morphology studies as to respond to the challenges posed by Big Data, and smart infrastructure. The proposed framework incorporates theoretical and modelling descriptions to verify how network-based models can act as the backbone skeletal representation of both building and urban complexity, and yet relate to environmental performance and smart infrastructure. The paper provides some empirical basis to support data information models through building dependency networks as to represent the relationships between different existing and smart infrastructure components. These dependency networks are thought to inform decisions on how to represent building and urban data sets in response to different social and environmental performance requirements, feeding that into void and solid descriptions of data maturity models. It is concluded that network-based models are fundamental to comprehend and represent the complexity of cities and inform urban design and public policy practices, in the design and operation phases of infrastructure projects

Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration

Chloroplast Sequence of Treegourd (Crescentia cujete, Bignoniaceae) to Study Phylogeography and Domestication

Premise of the study: Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). Methods and Results: Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated. By resequencing the whole chloroplast, we identified 66 SNPs in C. cujete (N = 30) and 68 SNPs in C. amazonica (N = 6). Nucleotide diversity was estimated at 1.1 × 10-3 and 3.5 × 10-3 for C. cujete and C. amazonica, respectively. Conclusions: This broadened C. cujete genetic toolkit will be important to study the origin, domestication, diversity, and phylogeography of treegourds in the Neotropics. © 2016 Moreira et al. Published by the Botanical Society of America

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