Use of DNA fingerprints to control the origin of sapelli timber (Entandrophragma cylindricum) at the forest concession level in Cameroon

Illegal logging and associated trade are the cause of many economic and ecological problems both in producer and in consumer countries. There are an increasing number of national and international regulations in place that call for efficient timber tracking systems. We present results of a pilot study of a DNA-based method to control the geographical origin of timber in forest concessions in Cameroon. We addressed genetic differentiation at five nuclear microsatellite loci in seven sapelli (Entandrophragma cylindricum, Meliaceae) populations located in three forest concessions in Eastern Cameroon. In the framework of a blind test, seven anonymous timber sample sets were analysed at three microsatellite loci and compared to the genetic reference data of the forest concessions in Cameroon. Our results show that genetic differentiation was low within and among concessions. Combining the results of Bayesian genetic assignment method and exclusion test, we could determine that the timber stemmed or did not stem from the focus forest concession in six out of the seven blind sample sets. We further discuss the accuracy of the presented method and draw conclusions for a better sampling and genotyping strategy. Our work provides clear evidence that the use of genetic fingerprints is a useful tool to fight against illegal logging.

Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity

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.

Transferability of Simple Sequence Repeat (SSR) Markers Developed in Litchi chinensis to Blighia sapida (Sapindaceae)

Ackee (Blighia sapida, Sapindaceae) is a multipurpose fruit tree species of high economic importance, native to the Guinean forests of West Africa, and belongs to the same family as that of lychee (Litchi chinensis). In this study, a set of 12 primer pairs for simple sequence repeats (SSRs) previously developed for lychee has been evaluated for polymorphism in 16 ackee trees from different populations. Seven primer pairs have been found to be transferable, and four have revealed polymorphisms. However, the average number of alleles per locus has dropped from 4.9 for lychee to 3.7 for ackee. Characterization of the four polymorphic markers in 279 individuals belonging to14 different ackee populations from Benin has revealed that the numbers of alleles per locus range from two to 14 with a mean number of 5.8. The observed and expected heterozygosities range between 0.020 to 0.359 and 0.020 to 0.396, respectively.

Cross-species transfer of nuclear microsatellite markers: potential and limitations

Molecular ecologists increasingly require 'universal' genetic markers that can easily be transferred between species. The distribution of cross-species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross-species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross-species transferable markers.

Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.)

In order to develop simple sequence repeat (SSR) markers in Italian ryegrass, we constructed a genomic library enriched for (CA)n-containing SSR repeats. A total of 1,544 clones were sequenced, of which 1,044 (67.6%) contained SSR motifs, and 395 unique clones were chosen for primer design. Three hundred and fifty-seven of these clones amplified products of the expected size in both parents of a two-way pseudo-testcross F(1) mapping population, and 260 primer pairs detected genetic polymorphism in the F(1) population. Genetic loci detected by a total of 218 primer pairs were assigned to locations on seven linkage groups, representing the seven chromosomes of the haploid Italian ryegrass karyotype. The SSR markers covered 887.8 cM of the female map and 795.8 cM of the male map. The average distance between two flanking SSR markers was 3.2 cM. The SSR markers developed in this study will be useful in cultivar discrimination, linkage analysis, and marker-assisted selection of Italian ryegrass and closely related species.

Monitoring genetic diversity in tropical trees with multilocus dominant markers

Since no universal codominant markers are currently available, dominant genetic markers, such as amplified fragment length polymorphism (AFLP), are valuable tools for assessing genetic diversity in tropical trees. However, the measurement of genetic diversity (H) with dominant markers depends on the frequency of null homozygotes (Q) and the fixation index (F) of populations. While Q can be estimated for AFLP loci, F is less accessible. Through a modelling approach, we show that the monolocus estimation of genetic diversity is strongly dependent on the value of F, but that the multilocus diversity estimate is surprisingly robust to variations in F. The robustness of the estimate is due to a mechanistic effect of compensation between negative and positive biases of H by different AFLP loci exhibiting contrasting frequency profiles of Q. The robustness was tested across contrasting theoretical frequency profiles of Q and verified for 10 neotropical species. Practical recommendations for the implementation of this analytical method are given for genetic surveys in tropical trees, where such markers are widely applied.

Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops

Model plants are facilitating the genetic characterization and comparative mapping of a number of traditional crops. Medicago truncatula has been widely accepted as a model plant to this end as it provides the essential tools for multiple aspects of legume genetics and genomics. A large set of markers from highly conserved M. truncatula gene regions is being created and used to establish a worldwide framework for comparative genomic studies in legumes. We have investigated the potential for cross-species amplification of 209 expressed sequence tag (EST)-based and 33 bacterial artificial chromosome (BAC)-based microsatellites from M. truncatula in the three most important European legume pulses-pea, faba bean and chickpea-that might facilitate future comparative mapping. Our results revealed significant transferability of M. truncatula microsatellites to the three pulses (40% in faba bean, 36.3% in chickpea and 37.6% in pea). The percentage of M. truncatula EST-SSRs (simple sequence repeats) amplified in the three crops (39-43%) was twofold higher than that of the genomic SSRs (21-24%). Sequence analysis determined that the level of conservation in the microsatellite motif was very low, while the flanking regions were generally well conserved. The variations in the sequences were mainly due to changes in the number of repeat motifs in the microsatellite region combined with indel and base substitutions. None of the functional microsatellites showed direct polymorphism among the parental genotypes tested, consequently preventing their immediate use for mapping purposes.

Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt-marsh species, we were interested in population differentiation through isolation-by-distance, and among strongly divergent habitats (low and high marsh) in this wind- and water-dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross-species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation-by-distance was present only on larger scales (60-443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation-by-distance) effects among six sites 2.5-443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection-mediated restrictions to gene flow simultaneously.

Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences

A total of 76 sweet cherry genotypes were screened with 34 microsatellite primer pairs previously developed in peach. Amplification of SSR loci was obtained for 24 of the microsatellite primer pairs, and 14 of them produced polymorphic amplification patterns. On the basis of polymorphism and quality of amplification, a set of nine primer pairs and the resulting 27 informative alleles were used to identify 72 genotype profiles. Of these, 68 correspond to unique cultivar genotypes, and the remaining four correspond to three cultivars that could not be differentiated from the two original genotypes of which they are mutants, and two very closely related cultivars. The mean number of alleles per locus was 3.7 while the mean heterozygosity over the nine polymorphic loci averaged 0.49. The results demonstrate the usefulness of cross-species transferability of microsatellite sequences allowing the discrimination of different genotypes of a fruit tree species with sequences developed in other species of the same genus. UPGMA cluster analysis of the similarity data divided the ancient genotypes studied into two fairly well-defined groups that reflect their geographic origin, one with genotypes originating in southern Europe and the other with the genotypes from northern Europe and North America.

Cross-species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: allelic polymorphism and degree of relationship

Microsatellite amplification was performed on cassava (Manihot esculenta) and six other different species (all wild) of the Manihot genus. We used ten pairs of microsatellite primers previously developed from cassava, detecting 124 alleles in a sample of 121 accessions of the seven species. The number of alleles per locus ranged from four to 21 alleles, and allelic diversity was greater in the wild species than in cassava. Seventy-nine alleles, including unique ones, were detected in the wild species but were not found in the crop. The lower level of heterozygosity in some wild species probably resulted from a combination of fine-scale differentiation within the species and the presence of null alleles. Overall, microsatellite primers worked across the genus, but, with increasing genetic distance, success in amplifying loci tended to decrease. No accession of M. aesculifolia, M. carthaginensis, and M. brachyloba presented a banding pattern at locus Ga-140; neither did one appear for M. aesculifolia at locus Ga-13. Previous work with amplified fragment length polymorphism (AFLP) markers and this microsatellite analysis show that these three wild taxa are the most distant relatives of the crop, whereas the wild forms M. esculenta subsp. flabellifolia and M. esculenta subsp. peruviana appear to be the closest.

Development and characterization of microsatellite markers for genetic analysis of a Brazilian endangered tree species Caryocar brasiliense

In this work we report the development and characterization of 10 microsatellite loci for the endangered tree species Caryocar brasiliense. Using genomic library enrichment, the efficiency of SSR marker development was 14.4% from sequencing data to operationally useful loci. Primer sequences for this set of 10 loci are made available together with their estimates of expected heterozygosity, probability of paternity exclusion and probability of identity. Mendelian inheritance and segregation was confirmed for all 10 loci in open-pollinated half-sib families as well as the absolute transferability of these 10 loci to five other species of the same genus. Number of alleles per locus ranged from 10 to 22 with a mean value of 16 and expected heterozygosity varying from 0.84 to 0.94. The combined probability of genetic identity was on the order of 10-17 clearly demonstrating that SSR multilocus genotypes are likely to be unique and capable of readily discriminating individuals of C. brasiliense. The very high combined probability of paternity exclusion (0.99999995) also indicates that these markers will permit detailed parentage studies in natural populations even in situations where both maternity and paternity are unknown. The battery of microsatellite markers developed and characterized in this study opens a new perspective for the generation of fundamental population genetic data for devising sound collection and conservation procedures for C. brasiliense and related species of the genus.

Gene-pool variation in caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple-sequence repeats

We have used polymorphic chloroplast simple-sequence repeats to analyse levels of genetic variation within and between seven native Scottish and eight mainland European populations of Scots pine (Pinus sylvestris L.). Diversity levels for the Scottish populations based on haplotype frequency were far in excess of those previously obtained using monoterpenes and isozymes and confirmed lower levels of genetic variation within the derelict population at Glen Falloch. The diversity levels were higher than those reported in similar studies in other Pinus species. An analysis of molecular variance (AMOVA) showed that small (3.24-8.81%) but significant (p < or = 0.001) portions of the variation existed between the populations and that there was no significant difference between the Scottish and the mainland European populations. Evidence of population substructure was found in the Rannoch population, which exhibited two subgroups. Finally, one of the loci studied exhibited an allele distribution uncharacteristic of the stepwise mutation model of evolution of simple-sequence repeats, and sequencing of the PCR products revealed that this was due to a duplication rather than slippage in the repeat region. An examination of the distribution of this mutation suggests that it may have occurred fairly recently in the Wester Ross region or that it may be evidence of a refugial population.