Kathleen Prinz

Identification of mango (Mangifera indica L.) landraces from Eastern and Central Kenya using a morphological and molecular approach

Local mangos (Mangifera indica L.) are highly valued for home consumption in rural Kenya and are regarded by the local population to be comparatively drought tolerant and less susceptible to pests and diseases than the improved varieties. These are characteristics which make them interesting for improvement and breeding purposes. To date, research on Kenyan mangos has mainly focused on introduced and commercial varieties, whereas information on local varieties and landraces is lacking. We present the first comprehensive morphological and molecular characterisation of local mango landraces from Eastern and Central Kenya. Thirty-eight local mango trees were sampled and characterized by 75 selected qualitative (44) and quantitative (31) morphological descriptors selected from the descriptor list developed for mango by Bioversity International (former IPGRI). Hierarchical cluster analysis was performed using first all variables and finally only 10 selected key descriptors. Additionally, dried mango leaves from the same 38 trees were used for molecular classification with 19 simple sequence repeat markers. Genetic relatedness between the mango samples was visualized using a dendrogram based on Nei’s genetic distance and Neighbor Joining methods. Morphological characterisation resulted in six distinct clusters, and molecular analysis in eight clusters, which partly supported the morphological classification. Four of the eight molecular clusters were consistent and molecular results confirmed morphological classification in these cases. Identification of local mango landraces using morphological traits can be considered as satisfying under field conditions, e.g. for rootstock identification in nurseries, but environmental conditions may influence the results. Molecular marker analysis is more expensive, but independent from environmental influences and thus suitable for identification of landraces in field genebanks and for breeding purposes. Outcomes of the present study can form the basis for urgently needed future conservation efforts, including circa situ conservation on farms and the development of ‘conservation through use’ strategies for local mango landraces in Kenya.

Genetic variation of teak (Tectona grandis Linn. f.) in Myanmar revealed by microsatellites

Genetic variation of teak (Tectona grandis Linn. f.) in 16 populations in Myanmar was investigated using ten nuclear microsatellite markers. Eight population pairs from two main regions in the north and the south of Myanmar were sampled. Each population pair consisted of an unlogged and a recently logged forest, each represented by 50 adult trees and 50 seedlings from the natural regeneration. For comparison, two land races from Benin (West Africa) were included. The major objectives of the study are to characterize the patterns of genetic variation of teak in natural populations, to examine genetic differentiation between adult trees and natural regeneration, and to investigate the impact of selective logging on genetic structures of teak. Genetic variation was high in all investigated populations. Slightly elevated levels of inbreeding were observed in the regeneration in comparison to the adults. Populations from the northern and the southern regions were strongly differentiated, but the differentiation between adults and natural regeneration and between unlogged and logged forests was low and not significant. Mantel tests indicated an isolation by distance (IBD) within the northern and the southern regions. High genetic diversity was also observed within the land races from Benin, which grouped to the southern populations. We failed to detect effects of logging on genetic diversity patterns or inbreeding in adults and regeneration, suggesting that high genetic diversity can even be sampled and maintained in disturbed forests. The observation of significant IBD and high differentiation between the populations of the north and the south of Myanmar suggests to include populations from widely separated forests in conservation programs, and to delineate provenance regions for the harvest and transfer of teak seeds and seedlings.

Genetic structure of disjunct Argentinean populations of the subtropical tree Anadenanthera colubrina var. cebil (Fabaceae)

Anadenanthera colubrina var. cebil is a native South American tree species inhabiting seasonally dry tropical forests (SDTFs). Its current disjunct distribution presumably represents fragments of a historical much larger area of this forest type, which has also been highly impacted by human activities. In this way the hypothesis of this study is that the natural populations of A. colubrina var. cebil from Northern Argentina represent vestiges of ancient fragmentation, but they are additionally influenced by a certain degree of gene flow among them. We aimed to analyze the genetic structure of both nuclear and chloroplast DNA to evaluate the relative role of ancient and recent fragmentation on intraspecific diversity patterns. Sixty-nine individuals of four natural populations were analyzed using eight nuclear microsatellites (ncSSR) and four chloroplast microsatellite loci (cpSSR). The level and distribution of genetic variation were estimated by standard population genetic parameters and Neighbor Joining as well as Bayesian analyses. The eight ncSSR loci were highly polymorphic, while genetic diversity of cpSSRs was low. Nuclear SSRs displayed lower genetic differentiation among populations than cpSSR haplotypes (FST 0.11 and 0.95, respectively). However, high differentiation between phytogeographic provinces was observed in both genomes. The high genetic differentiation detected emphasizes the role of ancient fragmentation. However, the Paranaense province also shows the effects of recent fragmentation on genetic structure, whereas gene flow by pollen preserves the effects of genetic drift in the Yungas province.

A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina

Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data, and two clusters were inferred. Individuals were assigned to their provinces of origin. Genetic molecular variation was higher in the populations of the Yungas biogeographic province which translates into highly qualified populations for conservation. Populations from the Paranaense biogeographic province showed the highest mean value of number of seeds per fruit making them valuable as well with regard to the exploitation of management strategies as a means to recover the impacted areas where these populations are located.

Development of microsatellite markers for Anadenanthera colubrina var. cebil (Fabaceae), a native tree from South America

PREMISE OF THE STUDY Microsatellite primers were developed in the native legume tree Anadenanthera colubrina var. cebil to study the genetic diversity and genetic structure in natural populations in Argentina. METHODS AND RESULTS Nine microsatellite markers were identified using a genomic library enriched for tandemly repeated motifs, eight of which markers were polymorphic. The polymorphism of these markers was assessed by investigating 20 individuals for fragment polymorphism; three to 13 alleles were observed for each locus. Observed and expected heterozygosities ranged from 0.300 to 1.000 and from 0.463 to 0.900, respectively. CONCLUSIONS These results confirm that these primers will be useful for investigating the genetic diversity and genetic structure of natural populations of A. colubrina var. cebil in future studies.

Genetic diversity in aspen and its relation to arthropod abundance.

The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen.

Genetic structure of coastal and inland populations of Spergularia media (L.) C. Presl (Caryophyllaceae) in Central Europe.

In Central Europe, salt-influenced habitats are restricted mainly to the coastlines of the North Sea and the Baltic Sea. The few natural inland salt sites suffer from size reduction and loss in biodiversity, while anthropogenic salt sites around potash mining dumps experienced recent and massive de novo colonization by numerous halophytes. Our study aimed to elucidate the general patterns of gene flow among coastal and inland salt habitats. We used amplified fragment length polymorphisms to assess the genetic diversity and genetic structure of 18 European populations of the halophyte Spergularia media (Caryophyllaceae), sampled from inland and coastal salt sites of Germany, the Netherlands, Denmark, Austria, France and Italy. Estimates of genetic diversity on the population level were generally low, especially within inland salt habitats. Analyses of molecular variance showed comparatively strong differentiation among populations. Multivariate ordination (principal coordinate analysis) and a NeighborNet analysis revealed four distinct groups of populations that showed good correspondence to their geographic origins. A Bayesian analysis performed with the program Structure as well as high pairwise ΦST values supported the results of the phenetic analyses. The observed patterns of diversity and differentiation among inland populations of S. media are best explained by the isolated nature of suitable salt habitats, with concomitant reduction of gene flow to and among these sites. Our data support the hypothesis that the colonization of anthropogenic salt sites by S. media originated from natural inland habitats.

Characterization and Transferability of Microsatellite Markers Developed for Carpinus betulus (Betulaceae)

Premise of the study: Carpinus betulus (Betulaceae) is an octoploid, ecologically important, common tree species in European woodlands. We established 11 nuclear microsatellite loci allowing for detailed analyses of genetic diversity and structure. Methods and Results: A microsatellite-enriched library was used to develop primers for 11 microsatellite loci that revealed high allele numbers and genetic diversity in a preliminary study. Conclusions: All of the loci developed here are informative for C. betulus. In addition, the loci are transferable to several species within the genus, and almost all loci cross-amplified in species of different genera of the Betulaceae.