Genetic diversity and demographic evolution of baobab (Adansonia digitata L., Bombacoideae, Malvaceae) populations in Senegalese Sahelian areas

This study evaluated the spatial genetic structure of baobab (Adansonia digitata L.) populations from three agroecological sites located in sahelian zone of Senegal using ITS1, 5.8S rDNA and ITS2 gene sequences. To determine the extent of isolation, gene sequences were analyzed between and among three sahelian baobab populations. At least 25 haplotypes of baobab (A. digitata L.) were revealed in Senegal (6, 9 and 10, respectively in Dakar, Bandia and Widou Thiengoly). Private haplotypes found in each locality show that there is an adaptation of the plant to environmental conditions prevailing in each site. Indeed, nucleotide diversity was more important in Dakar (0.00527); it ranges from 0.00483 to 0.00060 for Bandia and Widou populations, respectively. Curves of mismatch distribution show that the population of Ferlo has undergone a recent demographic expansion. Although Bandia and Dakar populations were polyphyletic; each shows a balanced expansion. Fst values ranging from 0.62946 to 0.90712 correlates a strong genetic differentiation between sites. A correlation between geographic and genetic distances was not highlighted by the Mantel’s test but phylogenetic trees of maximum likelihood and Bayesian inference have assigned two clades demonstrating that population of Ferlo (Widou) form a different ecotype from those of Bandia and Dakar.Keywords: ITS1, 5.8S, ITS2, Adansonia digitata, haplotype, genetic diversity, demographic evolutionAfrican Journal of Biotechnology Vol. 12(38), pp. 5627-563

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Cross-species amplification of microsatellite loci developed Digitaria exilis Stapf in related Digitaria species

Objectives: Digitaria exilis Stapf (white fonio) is a staple crop in West Africa, mainly consumed during food shortage and highly associated to cultural events. The aim of this study was to test the transferability of microsatellite loci developed for D. exilis to other species of the genus Digitaria in order to further investigate the diversity of species for which there is little genomic resources available.Methodology and Results : Eight (8) microsatellite loci on 119 accessions from 39 Digitaria species were tested. With an average amplification percentage of 62.8% ranging from 25% to 100 %, these SSR markers are transferable to other species of the genus Digitaria. The transferability was higher for D. argyrothrica, D.fuscescens, D. longiflora, D. milanjiana and D. ternata. In some species such as D. abyssinica, D. nuda, D. pennata, D. pseudodiagonalis and D. tisserantii, the very low percentage of cross-amplification confirmed their distance from D. exilis. D. longiflora, thought as the most related wild species to D. exilis, exhibited 100% level of transferable polymorphic loci.Conclusion and application of findings : This set of markers will be useful for breeding and studying relationships between Digitaria species.Keywords : Cross-species amplification, Digitaria, genetic diversity, microsatellite loci

Genetic diversity of Jatropha curcas L. in Senegal compared with exotic accessions based on microsatellite markers

International audienceSignificant efforts have been undertaken in West Africa to increase biofuel production with the expectation to alleviate the dependency on fossil energies and to reduce rural poverty by diversifying cultivated crops. In this context, Jatropha curcas L., a shrub belonging to Euphorbiaceae family, has gained great interest because of its oil which can be converted to biodiesel. It is also highly adaptable to marginal soils due to its drought-tolerant characteristics. Characterisation of J. curcas germplasm in Senegal could be an important input for its better management and in identifying genotypes that could be used in breeding program. Genetic diversity of 103 accessions including 82 accessions from different agro ecological zones in Senegal and 21 exotic accessions was assessed through 33 microsatellite markers. All the markers gave amplifications at the expected band size. Only one microsatellite marker, JCT17, was polymorphic showing 3 alleles and allows distinguishing 2 accessions from Burkina Faso. The surprisingly low level of genetic variation might be because introduction of J. curcas in Senegal seems to have been done from one or a few origins and the species has not regained genetic diversity since then due to vegetative propagation. Cultivation of J. curcas at large scale may face to vulnerability to pests and require many cautions. They are necessity to widen the genetic base of J. curcas in Senegal via new introductions from its centre of origin

GWAS unveils features between early- and late-flowering pearl millets

International audienceAbstract Background Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. Results We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass ( P -value < 2.3E-06). Conclusions The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species

Rainfed Food Crops in West and Central Africa: Points for Analysis and Proposals for Action

Ouvrage en libre accès, document disponible en ligne : http://www.afd.fr/webdav/site/afd/shared/PUBLICATIONS/RECHERCHE/Scientifiques/A-savoir/06-VA-A-Savoir.pdfInternational audienceThe rise in world agricultural prices in 2008 revealed the fragility of food security in many developing countries. Poor populations in sub-Saharan Africa are the biggest victims of this fragility. Rainfed food crops can play a unique role on the continent by supplying regional markets, increasing farmers' incomes, and creating jobs in rural areas. Working within the framework of the regional dynamics launched in West and Central Africa, AFD, CIRAD and IFAD initiated three studies to (i) map the food crop production and consumption areas in the zone, (ii) identify the contributions of research on these supply chains, and (iii) analyze food crop project practices. This book summarizes this research, accomplished with African research and regional expertise centers (AGRHYMET, WECARD). It reports on current knowledge of the main food crop supply chains in the region: rice, corn, cassava, millet-sorghum, yam, groundnut and cowpea. Other areas remain to be explored to strengthen existing dynamics: how can intermediation professions be supported? How can a regional approach to these supply chains be developed so as to disseminate best practices, expand markets and foster synergy? What role in supporting these supply chains could be (re)assigned to research? How can the financing constraint, which is present throughout the supply chain, be overcome? This book aims to provide keys to decipher supply chain operations and the challenges facing food crop supply chains in this region