Genetic diversity and core subset selection in ex situ seed collections of the banana crop wild relative Musa balbisiana

Crop wild relatives (CWRs) play a key role in crop breeding by providing beneficial trait characteristics for improvement of related crops. CWRs are more efficiently used in breeding if the plant material is genetically characterized, but the diversity in CWR genetic resources has often poorly been assessed. Seven seed collections of Musa balbisiana, an important CWR of dessert and cooking bananas, originating from three natural populations, two feral populations and two ex situ field collections were retrieved and their genetic diversity was quantified using 18 microsatellite markers to select core subsets that conserve the maximum genetic diversity. The highest genetic diversity was observed in the seed collections from natural populations of Yunnan, a region that is part of M. balbisiana's centre of origin. The seeds from the ex situ field collections were less genetically diverse, but contained unique variation with regards to the diversity in all seed collections. Seeds from feral populations displayed low genetic diversity. Core subsets that maximized genetic distance incorporated almost no seeds from the ex situ field collections. In contrast, core subsets that maximized allelic richness contained seeds from the ex situ field collections. We recommend the conservation and additional collection of seeds from natural populations, preferentially originating from the species' region of origin, and from multiple individuals in one population. We also suggest that the number of seeds used for ex situ seed bank regeneration must be much higher for the seed collections from natural populations

When xylarium and herbarium meet : linking Tervuren xylarium wood samples with their herbarium specimens at Meise Botanic Garden

Background: The current data paper aims to interlink the African plant collections of the Meise Botanic Garden Herbarium (BR) and the Royal Museum for Central Africa Xylarium (Tw). Complementing both collections strengthens the reference value of each institutional collection, as more complete metadata are made available and it enables increased quality control for the identification of wood specimens. Furthermore, the renewed connection enables the linking of available wood trait data with data on phenology, leaf morphology or even molecular information for many tree species, allowing assessments of performance of individual trees. In addition to studies at the interspecific level, comparisons at the intraspecific level become possible, which could lead to important new insights into resilience to and impact of global change, as well as biodiversity conservation or forest management of Central African forest ecosystems. New information: By interlinking the Tervuren Xylarium Wood database with the recently digitised herbarium of Meise Botanic Garden, we were able to establish a link between 6,621 xylarium and 9,641 herbarium records for 6,953 plant specimens. Both institutional databases were complemented with reliable specimen metadata. The Tervuren xylarium now profits from taxonomic revisions made by botanists at Meise Botanic Garden and a list of phenotypical features for woody African species can be extended with wood anatomical descriptors. New metadata from the Tw xylarium records were used to add the country of collection to 50 linked BR herbarium specimens for which this information was missing. Furthermore, metadata available from the labels on digitised BR herbarium specimens was used to update Tw xylarium records with the date of collection (817 records), collection locality (698 records), coordinates (482 records) and altitude (817 records). In conclusion, we created a reference database with reliable botanic identities which can be used in a range of studies, such as modelling analyses, community assessments or trait analyses, all framed in a spatiotemporal context. Furthermore, the linked collections hold historical reference data and specimens that can be studied in the context of global changes

A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology

Comparative phylogeography of widespread tree species from the Congo Basin

The aim of this PhD study was to gain new insights into the evolutionary history of the Central African rainforests, which are among the most complex and diverse ecosystems on earth. Even today, many questions regarding the underlying dynamics and evolutionary processes shaping that remarkable diversity remain unanswered, since relatively few studies have focused on the vast tropical forests growing in the Congo Basin. Therefore, we applied various molecular approaches to study the levels of genetic diversity and patterns of differentiation within and between population of the tropical tree species Scorodophloeus zenkeri, Staudtia kamerunensis and Prioria balsamifera. In Chapter 2, we conducted a phylogeographic study on the widespread tropical tree Scorodophloeus zenkeri to assess the impact of past forest fragmentation in Central African lowland forests. By applying Bayesian clustering methods, we revealed six intraspecific genetic clusters within the species. The observed genetic discontinuities most likely result from forest fragmentation during the glacial periods of the Pleistocene. Populations in Lower Guinea appeared differentiated from those in Congolia, and both bioregions harboured distinct genetic clusters.In Chapter 3, we developed 16 highly polymorphic microsatellite primers (SSRs) for Staudtia kamerunensis, a timber species for which species-specific genetic markers were lacking. By validating the developed markers in three populations, we demonstrated their usefulness to study gene flow, population structure and spatial distribution of genetic diversity in S. kamerunensis.In Chapter 4, we applied the newly developed SSRs, two nuclear gene markers and a chloroplast marker to search for evolutionary lineages in Staudtia kamerunensis, a species with a complex taxonomical history. Our analyses reveal multiple genetic discontinuities among populations throughout Central Africa, probably resulting from ancient rainforest fragmentation during cold and dry periods in the Pliocene and/or Pleistocene. However, the clear genetic disjunction observed between northern and southern populations in Lower Guinea could correspond to a genetic break between the kamerunensis and gabonensis varieties described in Staudtia kamerunensis.In Chapter 5, we developed two new sets of microsatellite primers (SSRs); 16 primer pairs for Prioria balsamifera and 15 primer pairs for Prioria oxyphylla. Validation of the primers in two populations of each species, as well as the cross-amplification tests, demonstrated the usefulness of the SSRs to study gene flow and spatial genetic structure in African Prioria species, which is needed to prevent genetic erosion and to set up proper conservation guidelines.In Chapter 6, the 16 newly developed microsatellite loci were amplified in individuals of P. balsamifera from Gabon and the Democratic Republic of the Congo, to assess the levels of genetic diversity and intraspecific differentiation. Our analyses show that the genetic diversity in P. balsamifera populations is relatively low, so efforts should be made to prevent further depletion of the gene pool. Bayesian clustering analyses revealed multiple genetic discontinuities throughout the Congo Basin, probably caused by ancient forest fragmentation. The inferred intraspecific clusters show a parapatric distribution, so they can potentially be used to determine the origin of individuals at a regional scale. Additionally, various genetic assignment methods show that the SSR dataset generated in this study can be used as a reference database for Gabon and DR Congo. The general discussion allows us to show similarities in the genetic structures of species that can be interpreted in terms of forest cover history in Central Africa.Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Isolation of microsatellite loci in the African tree species Staudtia kamerunensis (Myristicaceae) using high-throughput sequencing

Staudtia kamerunensis (Myristicaceae) or ‘Niové’ is an evergreen tree widespread in Central African moist forests. The bark and seeds are used in traditional medicine, yet the tree is mainly harvested for its high quality, multi-purpose timber. To facilitate sustainable harvesting and conservation of the species, we aim to develop microsatellite markers that can be used to study the mating system, gene flow, genetic diversity and population structure. Genomic DNA of S. kamerunensis was sequenced on an Illumina MiSeq platform, generating 195,720 paired-end reads with 3671 sequences containing microsatellites. Amplification tests resulted in the development of 16 highly polymorphic microsatellite loci of which 14 were tested in 183 individuals of S. kamerunensis from three populations. The number of detected alleles per locus ranged from 15 to 39 and the average observed and expected heterozygosity across loci and populations were Ho = 0.713 (0.14–0.97) and He = 0.879 (0.19–0.95) respectively. The high levels of polymorphism observed in the newly developed microsatellite markers demonstrate their usefulness to study gene flow, population structure and spatial distribution of genetic diversity in S. kamerunensis.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Evidence of past forest fragmentation in the Congo Basin from the phylogeography of a shade-tolerant tree with limited seed dispersal: Scorodophloeus zenkeri (Fabaceae, Detarioideae)

Background: Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. Results: Clear intraspecific genetic discontinuities occur throughout the species’ distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. Conclusions: Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla

status: publishe

Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla

Research Highlights: Two novel sets of polymorphic microsatellite markers were developed for Prioria balsamifera and Prioria oxyphylla through high-throughput sequencing. Validation in two populations of each species proved the utility of the developed primers to estimate genetic diversity at population level. Background and Objectives: Prioria balsamifera and Prioria oxyphylla are tropical tree species from Central Africa. They produce a high-quality, multi-purpose timber that is of great interest to the international market. Prioria balsamifera has been included as ‘endangered’ on the IUCN Red List of Threatened Species. In order to set up adequate management plans and facilitate timber tracking, knowledge on the genetic diversity at population level is needed. Therefore, we aim to develop microsatellite markers that can be used for species conservation, forensics, plant breeding and population genetics studies. Materials and Methods: Genomic DNA of P. balsamifera and P. oxyphylla was sequenced on an Illumina NextSeq platform (Illumina Inc. San Diego, CA, USA), generating 829,421 and 772,018 paired-end reads that contained 7148 and 7004 microsatellite sequences, respectively. The QDD-pipeline was used to design primers, which were tested for amplification in two populations of each species. Cross-species amplification was tested in all seven African Prioria species. Results: For P. balsamifera, 16 polymorphic microsatellite markers were developed and combined in three multiplexes. Inbreeding appeared to be absent but genetic diversity was low in both populations. For P. oxyphylla, 15 polymorphic microsatellite markers were developed and combined in three multiplexes. Genetic diversity was low in both populations and estimated null allele frequencies were high for multiple loci. Cross-species amplification tests demonstrated the occurrence of conserved loci that amplified for most of the African Prioria species. Conclusions: The microsatellite markers prove to be useful for estimating genetic diversity at population level. These novel markers can be used to study gene flow and spatial genetic structure in Prioria species, which is needed to set up proper conservation guidelines and to prevent genetic erosion.info:eu-repo/semantics/publishe

Spatial variability of iron, zinc and selenium content in faba bean (Vicia faba L.) seeds from central and southwestern highlands of Ethiopia

Aims This study has been carried out to determine the spatial variability of faba bean seed Fe, Zn and Se content across agro-ecological zones in central and southwestern Ethiopia, where it is an important source of protein in the diet. The study assessed whether soil properties, arbuscular mycorrhizal fungi (AMF), faba bean characteristics and genetic diversity and agro-ecological zone as random factor affect seed Fe, Zn and Se content. Methodology Multi-location fields were sampled in three important faba bean growing agro-ecologies during the 2018-2019 cropping season. Results Seed Fe content varied from 45.7-61.9, 41.6-102 and 31.1-77.0 mg kg(-1) in Cheliya, Dedo and Dendi, respectively. Likewise, Zn content ranged from 38.3-56.3, 44.6-73.6 and 21.6-49.9 mg kg(-1). Selenium content varied from 10.1-45.1, 12.1-160 and 16.2-167 mu g kg(-1). Significant differences were observed for Zn and Se content across agro-ecologies. Consumption of 100 g faba beans per day can provide an overall average of 64 and 28% of the recommended daily allowance (RDA) for Fe, 45 and 62% for Zn and only 8% for Se for male and female adults, respectively. Soil properties explained seed Fe, Zn and Se content variation. However, for Zn and Se content the largest share of the difference was explained by agro-ecological mediated environmental variations. As a consequence, differences in dietary intake of micro-nutrients via faba beans are determined by living area. Conclusion Soil properties and especially agro-ecological mediated environmental conditions explained seed Zn and Se content of faba bean and hence potential dietary intake

Genetic diversity and core subset selection in ex situ seed collections of the banana crop wild relative Musa balbisiana

Open Accessstatus: Published onlin