Genetic diversity and differentiation among the species of African mahogany (Khaya spp.) based on a large SNP array (original) (raw)
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Molecular markers for Khaya senegalensis, an important forestry tree species
SABRAO journal of breeding and genetics
Khaya senegalensis (African mahogany or dry-zone mahogany) is a highvalue hardwood timber species with great potential for forest plantations in northern Australia. Currently the Northern Territory -Queensland governments' breeding program, based on a large number of provenance introductions from the native range of central African countries in the late 1960's and 1970's, is the largest known domestication program for this species. This program has involved assessment of open pollinated seedlings and resulted in more than 50 clones selected for commercialisation. A lack of DNA molecular markers has hampered assessment of genetic diversity within the provenance collection. We are developing DNA markers including microsatellites, Sequence Characterised Amplified Regions and Single
Genetics and Molecular Biology
Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Pará. These populations are among the oldest plantations (>15 years) in Brazil and, therefore, the country's main seed sources. The average number of alleles per locus was 5.9, expected heterozygosity was moderate (H E =0.56) and lower than the high observed heterozygosity (H O =0.74). Therefore, the intrapopulation fixation index was negative (f=-0.31) indicating the possibility that selection of superior trees might have favored heterozygous plants with heterosis. No genetic structure was observed between provenances. The genetic diversity observed within selected trees, with an effective population size (Ne) of 30.4, is comparable to that of natural populations of African and Brazilian mahoganies. Therefore, our results contradict the idea that the genetic diversity of K. grandifoliola introduced in Brazil is low and show that our germplasm can be exploited for breeding purposes.
CpDNA-based species identification and phylogeography: application to African tropical tree species
Molecular Ecology, 2010
Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations.
Molecular Ecology Resources, 2012
Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93 943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.
Notulae Scientia Biologicae
There are over 8,000 globally threatened tree species. For each species, there is a different story behind why they are threatened and what values we stand to lose if we do not find the means to save them. Mahogany, a member of Meliaceae, is a small genus with six species. Its straight, fine and even grain, consistency in density and hardness makes it a high valued wood for construction purposes. The bitter bark is widely used in traditional medicine in Africa. The high demand for bark has also led to the total stripping of some trees, complete felling of larger trees to get the bark from the entire length of the tree and bark removal from juvenile trees. These species are now threatened with extinction due to selective and polycyclic logging, and also excessive bark removal. The natural regeneration of mahogany is poor, and mahogany shoot borer Hypsipyla robusta (Moore) attacks prevent the success of plantations within the native area in West Africa. In developing countries, most o...
Heredity, 1999
Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra-and interpopulation variance coecients, by analysis of molecular variation (AMOVA AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also re¯ected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging signi®cantly decreased population diversity (P 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It oers practical information for the future conservation of mahogany and highlights some factors that may have in¯uenced the partitioning of genetic diversity in this species across Mesoamerica.
We review here the scale of neutral and adaptive genetic variation of mahogany (Swietenia spp.), one of the most valuable tree species in the world, and relate this information directly to provenance performance, and seed transfer and sourcing recommendations. Further, we explore a series of scientific issues directly related to critical day-to-day management of mahogany, giving guidelines to maximise genetic diversity outcomes in natural, remnant, sustainably harvested, and/or restored forest landscapes. The study concludes that conservation and sustainable management of mahogany genetic resources cannot be simply defined in terms of one-size-fits-all solutions, and requires local community involvement to prevent illegal logging and ensure mutual benefit. Landscape level strategies for the effective management of mahogany trees outside of forests urgently need to be developed, together with strategies to promote the benefits of different agroforestry practices. There is also a requirement for conservation planners to consider that trees found outside protected areas have a role in the conservation. In wide-ranging species, promoting international collaboration for collecting, characterising, and conserving genetic resources is vital as international consensus is needed to streamline phytosanitary procedures, to facilitate the exchange of forest reproductive material, and assist genetic resource conservation efforts.
Mahogany as a genetic resource
Botanical Journal of The Linnean Society, 1996
The development of a strategy for the sustainable management and conservation of mahogany is an urgent priority. Such a strategy should be based upon clear information about the extent of genetic differentiation within and between populations, and on an understanding of the processes maintaining this variation. At present, such information is very limited for mahogany. Preliminary data are presented from two genetic tests of Szmitaia muoophyllu King (Meliaceae), indicating significant differences between provenances and half-sib progenies in both growth and form characteristics. In addition, the use of molecular markers for the characterization of genetic resources of mahogany is discussed. On the basis of the results available, the impacts of deforestation and logging activities on genetic resources are evaluated. Although both deforestation and selective logging may deplete genetic resources, no quantitative information on the extent of such depletion in mahogany is currently available. Additional research is therefore required before clear guidelines can be provided for the sustainable management of mahogany.
Tropical Conservation Science, 2016
The montane forests of southeastern Nigeria are of immense conservation value due to their high levels of biodiversity and endemism. Yet despite increasing anthropogenic disturbance and forest fragmentation, little is known about the genetics of resident tree populations. We used a set of conserved chloroplast simple sequence repeat (SSR) primers to quantify and directly compare genetic diversity in three tree species: Cordia millenii, West African Cordia; Entandrophragma angolense, tiama mahogany; and Lovoa trichilioides, African walnut, within a single montane forest. Additionally, we assessed the diversity of West African Cordia between forests at a local and regional scale. Results indicate that for our focal loci, in all three species, there is a general lack of chloroplast genetic diversity. Our study is particularly relevant because it considers genetic diversity among multiple tree species simultaneously. This work represents the first study of its kind in the region, and will pioneer the way for future conservation genetic studies in montane Nigeria.
Genetic Variation in Tropical Tree Species and Plantations: A Review
Open Journal of Forestry, 2022
The global efforts to restore tropical forests and their productive and ecological functions through plantation forestry largely depend on the available genetic variation in the tree species used to establish the plantations. However, there is limited information on the levels and trends of the genetic variation and variability of different plantation tree species in the tropics. Therefore, this study reviews several marker-based studies that have investigated genetic variation. Most of the top economic species like Eucalyptus tereticornis and Mansonia altissima are attributed to low levels of genetic diversity, while others like Pinus caribaea and Swietenia macrophylla still exhibit high expected heterozygosity across different populations. However, the levels of genetic diversity assessed may depend on the markers used. Microsatellites, i.e., simple sequence repeats (SSRs), mostly give higher estimates when compared to other polymerase chain reaction-based markers. Other factors that typically contribute to the directional pattern of genetic variation in tropical tree species and populations include their distribution, density, seed dispersal, succession, and reproduction. Also, anthropogenic impacts like logging and fragmentation have contributed to the vast genetic base reduction of many tropical species and populations. Having adequate genetic variation within the plantation populations is significant in improving their fitness, resilience, fecundity, productivity, and other ecological functions. It also provides a basis for tree improvement and breeding in plantation forests. Although clonal forestry is becoming widespread and considered highly productive, it is attributed to specific economic, technical, and ecological risks, such as the increased spread of pests and diseases. Therefore, further discussions and recommendations to maximise genetic diversity in tropical (clonal) plantations are provided.