Microsatellite variation and population structure of a recovering Tree frog (Hyla arborea L.) metapopulation

Numbers and sizes of populations of the European tree frog in The Netherlands have dramatically decreased in the second half of the last century due to extensive habitat destruction and fragmentation. We have studied the genetic structure of a slowly recovering meta-population. Strong genetic differentiation, estimated at eight microsatellite loci, was found between clusters of populations (F _st-values above 0.2). Within clusters, consisting of ponds within a radius of about 5 km, European tree frog populations were less differentiated (F _st<0.08) and exact tests showed that most of the ponds within clusters were not significantly differentiated. Although local population sizes have been increasing since 1989, and some new ponds have been colonised in the direct vicinity of ponds that have been populated continuously, little evidence for gene flow between clusters of ponds was found (only one exception). Furthermore, levels of genetic diversity were low compared to populations in comparable areas elsewhere in Europe. Therefore, a continuous conservation effort is needed to prevent any further loss of genetic diversity. The alleviation of important barriers to dispersal between the clusters should be given a high priority for the restoration of the meta-population as a whole.     

链霉菌次级代谢产物高产菌株的构建策略

随着基因测序技术的发展,人类获得了大量有关链霉菌次级代谢产物合成基因簇的信息,通过合理的构建策略可以激活其中的隐性基因簇或提高基因簇的表达水平,从而获得新的链霉菌次级代谢产物,或显著提高已知次级代谢产物的发酵水平。从基因表达调控、转座子突变、合成生物学方法、组学方法等四个方面,综述了提高链霉菌次级代谢产物产量的构建策略及其研究进展。     

Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial‐genetic patterns of connectivity

Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within‐species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population‐level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G”_ST) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G”_ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species.     

Understanding and manipulating glycopeptide pathways: the example of the dalbavancin precursor A40926

Glycopeptide antibiotics represent an important class of microbial compounds produced by several genera of actinomycetes. The emergence of resistance to glycopeptides among enterococci and staphylococci has prompted the search for second-generation drugs of this class and semi-synthetic derivatives are currently under clinical trials. Dalbavancin is obtained by chemical modification of the natural glycopeptide A40926, produced by a Nonomuraea sp. Recently, there has been considerable progress in the elucidation of biosynthesis of glycopeptide antibiotics; several gene clusters have been characterized, thus providing an understanding of the biosynthesis of these chemically complex molecules. Furthermore, such investigations have yielded the first glycopeptide derivatives produced by genetic or enzymatic intervention. We have isolated and characterized the dbv clusters, involved in the formation of the glycopeptides A40926. The development of a gene-transfer system for Nonomuraea sp. has allowed the manipulation of the A40926 pathway. New derivatives were obtained by inactivating selected dbv genes. In addition, our data suggest differences in the biosynthetic routes for heptapeptide formation between the vancomycin and the teicoplanin families of glycopeptides.     

Genetic diversity of Syrian Arabian horses

Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (H_o) ranged between 0.30 and 0.32, expected heterozygosity (H_e) between 0.30 and 0.31 and inbreeding coefficients (F_is) between ?0.02 and ?0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (F_st < 0.05). Hierarchical clustering showed a clear distinction between Arabian and Przewalski's horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub‐clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity.     

Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation

Traditional methods for characterizing genetic differentiation among populations rely on a priori grouping of individuals. Bayesian clustering methods avoid this limitation by using linkage and Hardy–Weinberg disequilibrium to decompose a sample of individuals into genetically distinct groups. There are several software programs available for Bayesian clustering analyses, all of which describe a decrease in the ability to detect distinct clusters as levels of genetic differentiation among populations decrease. However, no study has yet compared the performance of such methods at low levels of population differentiation, which may be common in species where populations have experienced recent separation or high levels of gene flow. We used simulated data to evaluate the performance of three Bayesian clustering software programs, PARTITION, STRUCTURE, and BAPS, at levels of population differentiation below F _ST=0.1. PARTITION was unable to correctly identify the number of subpopulations until levels of F _ST reached around 0.09. Both STRUCTURE and BAPS performed very well at low levels of population differentiation, and were able to correctly identify the number of subpopulations at F _ST around 0.03. The average proportion of an individual’s genome assigned to its true population of origin increased with increasing F _ST for both programs, reaching over 92% at an F _ST of 0.05. The average number of misassignments (assignments to the incorrect subpopulation) continued to decrease as F _ST increased, and when F _ST was 0.05, fewer than 3% of individuals were misassigned using either program. Both STRUCTURE and BAPS worked extremely well for inferring the number of clusters when clusters were not well-differentiated (F _ST=0.02–0.03), but our results suggest that F _ST must be at least 0.05 to reach an assignment accuracy of greater than 97%.     

Effective selection and regeneration of transgenic rice plants with mannose as selective agent

A new method for the selection of transgenic rice plants without the use of antibiotics or herbicides has been developed. The phosphomannose isomerase (PMI) gene from Escherichia coli has been cloned and consitutively expressed in japonica rice variety TP 309. The PMI gene was transferred to immature rice embryos by Agrobacterium-mediated transformation, which allowed the selection of transgenic plants with mannose as selective agent. The integration and expression of the transgene was confirmed by Southern and northern blot analysis and the activity of PMI indirectly proved with the chlorophenol red assay. The results of genetic analysis showed that the transgenes were segregated in a Mendelian fashion in the T₁ generation. The establishment of this selection system in rice provides an efficient way for producing transgenic plants without using antibiotics or herbicides with a transformation frequency of up to 41%.     

Genetic substructure and admixture as important factors in linkage disequilibrium‐based estimation of effective number of breeders in recovering wildlife populations

The number of effective breeders (N_b) and effective population size (N_e) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium‐based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993–2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on N_b and N_e, by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for N_e were larger than N_b and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of N_b and N_e. Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on N_b and N_e.     

Microsatellite markers reveal two admixed genetic groups and an ongoing displacement within the French population of the invasive plant pathogen Phytophthora infestans

Potato late blight is an example of a re‐emerging disease of plants. Phytophthora infestans was first introduced into Europe during the 19th century, where it caused the Irish potato famine. During the 20th century several additional introduction events have been suspected, especially in the mid‐70s due to the import of large quantities of potato needed after the shortage caused by drought in 1976. Here, we investigate the genetic population structure of Phytophthora infestans, at the first stages of a recent invasion process in France. A total of 220 isolates was collected from 20 commercial fields of the potato susceptible cultivar Bintje, during two consecutive years (2004 and 2005). Clustering analyses based on eight recently developed microsatellite markers reveal that French P. infestans populations are made of two differentiated genetic clusters of isolates (F_ST = 0.19). This result suggests multiple introductions of P. infestans into France, either through the introduction of a composite population of isolates or through the successive introduction of isolates having differentiated genetic backgrounds. Both clusters identified have a strong clonal structure and are similar regarding genetic diversity and mating type composition. The maintenance of differentiation between the two genetic clusters should result from the low or non‐existent contribution of sexual reproduction in French P. infestans populations.     

Population structure,dispersal and colonization history of the garden bumblebee <Emphasis Type="Italic">Bombus hortorum</Emphasis> in the Western Isles of Scotland

New methods of analysing genetic data provide powerful tools for quantifying dispersal patterns and reconstructing population histories. Here we examine the population structure of the bumblebee Bombus hortorum in a model island system, the Western Isles of Scotland, using microsatellite markers. Following declines in other species, B. hortorum is the only remaining long-tongued bumblebee species found in much of Europe, and thus it is of particular ecological importance. Our data suggest that populations of B. hortorum in western Scotland exist as distinct genetic clusters occupying groups of nearby islands. Population structuring was higher than for other bumblebee species which have previously been studied in this same island group (F_st = 0.16). Populations showed significant isolation by distance. This relationship was greatly improved by using circuit theory to allow dispersal rates to differ over different landscape features; as we would predict, sea appears to provide far higher resistance to dispersal than land. Incorporating bathymetry data improved the fit of the model further; populations separated by shallow seas are more genetically similar than those separated by deeper seas. We argue that this probably reflects events following the last ice age when the islands were first colonized by this bee species (8,500–5,000 ybp), when the sea levels were lower and islands separated by shallow channels would have been joined. In the absence of significant gene flow these genetic clusters appear to have since diverged over the following 5,000 years and arguably may now represent locally adapted races, some occurring on single islands.     

The photosynthetic stress responses of five pepper species are consistent with their genetic variability

The aim of the study was to investigate the genetic distances and their relationships among pepper species using photosynthetic features under different stresses and genetic variability. The photosynthetic features under drought, waterlogging and low-temperature stresses, rDNA internal transcribed spacer (ITS) sequences of nuclear genome and trnH-psbA sequence of chloroplast genome of 25 varieties from 5 pepper species Capsicum annuum L. (CA), Capsicum baccatum L. (CB), Capsicum chinense Jacquin. (CC), Capsicum frutescens L. (CF) and Capsicum pubescens Ruiz & Pavon (CP) were analyzed and used to construct the dendrograms. The results showed the photosynthetic rate of different pepper species could be greatly but differentially decreased by stresses. For example, CB and CF had the smallest and the highest decrease to drought, CC had the highest decrease to waterlogging, and CP had the smallest decrease to low temperature. The ITS sequences of 25 pepper varieties are 591–619 bp in length and have GC% between 51.1% and 64.5%. Their trnH-psbA sequences are 537–558 bp in length and have GC% between 27.2% and 28.5%. The cluster analysis of the five pepper species based on the changes in P _N under stresses is similar to that based on genetic variability, that is, CP clusters with CB, and CC clusters with CA after first clusters with CF. In addition, the clustering methods based on the photosynthetic stress responses and genetic variability are unable to completely distinguish pepper varieties within the same species. The results indicate that similarly to genetic variability, changes in P _N under stresses (specifically the stress corresponding to the climate of plant’s original habitat) could be used to identify genetic distance of pepper species.     

BIOTYPING CONFIRMS A NEARLY CLONAL POPULATION STRUCTURE IN ESCHERICHIA COLI

A. reference collection of 72 natural isolates of Escherichia coli (the ECOR collection) has been examined with respect to eight metabolic capabilities (biotype characters) plus motility and resistance or sensitivity to five common antibiotics. Data from biotype characters were analyzed by means of unweighted pair-group cluster analysis, and the genetic variation among the strains defines three major clusters of strains with substantial variation within each cluster but greater genetic similarity of strains within a cluster than between clusters. These clusters define an infraspecific population structure in E. coli, which reflects the predominantly clonal mode of reproduction in this organism. The clusters identified by the biotype characters are in good agreement with those resulting from an analysis of 11 enzyme polymorphisms (allozymes) among the strains, and these are in good agreement with the infraspecific structure detected by factor analysis of allozyme data. The clusters of strains also differ in several genetic characteristics that are independent of those used in making the classification.     

Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple

Malus sieversii (Lebed.) M. Roem. is a wild progenitor species of the domesticated apple. It is found across a mountainous region of central Asia and has been the focus of several collection expeditions by the USDA-ARS-National Plant Germplasm System. This study used microsatellite variation at seven loci to estimate diversity and differentiation within M. sieversii using several complimentary approaches. Multilocus genotypes were amplified from 949 individuals representing seedling trees from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Apportioning of genetic variation was estimated at both the family and site level. Analyses using a hierarchical model to estimate F _st showed that differentiation among individual families is more than three times greater than differentiation among sites. In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network among all sites showed that differentiation is largely congruent with geographical location. In addition, nonhierarchical Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters in the data set. The quality of these assignments was evaluated over multiple Markov Chain Monte Carlo runs using both posterior likelihood and stability of the assignments. The spatial pattern of genetic assignments among the eight collection sites shows two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites are more admixed and more diverse than the northern sites.     

Polyploid origin,genetic diversity and population structure in the tetraploid sea lavender <Emphasis Type="Italic">Limonium narbonense</Emphasis> Miller (Plumbaginaceae) from eastern Spain

Limonium narbonense Miller is a fertile tetraploid species with a sporophytic self-incompatibility system. This sea lavender is found in coastal salt marshes which have been under intense human pressure during the past decades resulting in significant habitat fragmentation. Eleven microsatellite loci specifically designed for this species were amplified in 135 individuals from five populations. These markers were used to investigate the polyploid nature, the levels of genetic diversity and population structure in this species. L. narbonense showed high levels of genetic diversity (A = 7.82, P = 100% H _T = 0.446), consistent with its likely autotetraploid origin revealed in this study and obligate outcrossing breeding system. Inbreeding (F _IS) values were low in the three southern populations (mean F _IS = 0.062), and higher in the northern populations (mean F _IS = 0.184). Bayesian analysis of population structure revealed that populations could be grouped into two genetic clusters, one including three southern populations and the other the two northernmost ones. Individuals from the two northernmost populations showed higher admixture of the two genetic clusters than individuals from the three southern ones. A thorough analysis of microsatellite electrophoretic patterns suggests an autotetraploid origin for L. narbonense. The genetic structure revealed in this study is attributed to a recent migration from the southern area. This result suggests a net gene flow from the south to the north, likely facilitated by migratory movements of birds visiting the temporary flooded ponds occupied by L. narbonense.     

New aspects of genes and enzymes for β-lactam antibiotic biosynthesis

Penicillins, cephalosporins and cephamycins are peptide antibiotics synthesized by condensation of l-α-aminoadipic acid, l-cysteine and l-valine to form the tripeptide δ(l-α-aminoadipyl)-l-cysteinyl-d-valine (Aad-Cys-Val) by a non-ribosomal peptide synthetase. The genes pcbAB and pcbC, common to all penicillin and cephalosporin producers, that encode the Aad-Cys-Val synthetase¹ and isopenicillin N (IPN) synthase¹ respectively, have been cloned and the encoded enzymes studied in detail. The IPN synthase has been crystallized and its active center identified, providing evidence for the molecular mechanism of cyclization of the tripeptide Aad-Cys-Val to isopenicillin N. The late genes of the penicillin and cephalosporin pathways have also been characterized although some of the molecular mechanisms catalyzed by the encoded enzymes (e.g. IPN acyltransferase) are still obscure. In cephamycin-producing organisms, biosynthesis of the α-aminoadipic acid precursor proceeds in two steps catalyzed by lysine 6-aminotransferase and piperideine-6-carboxylic acid dehydrogenase. The gene lat for the first of these enzymes is located in the cephamycin gene cluster, providing an interesting example of association of genes encoding enzymes for the formation of a precursor with genes involved in assembly of the antibiotics. Novel enzymes involved in methoxylation at C-7 and carbamoylation at C-3′ of the cephem nucleus were isolated from Nocardia lactamdurans and Streptomyces clavuligerus. The methoxylation system is encoded by two linked genes cmcI-cmcJ and their products (proteins P₇ and P₈) form a complex that is required for hydroxylation at C-7 and for the subsequent methylation of the 7-hydroxycephem derivative to form the methoxyl group. Carbamoylation at the C-3′-hydroxyl group of the cephem nucleus is catalyzed by a specific carbamoyltransferase encoded by the gene cmcH. Finally, genes for a β-lactamase (bla), a penicillin-binding protein (pbp) and a transmembrane protein (cmcT) that appears to be involved in cephamycin exportation, are clustered together with the biosynthetic genes in the cephamycin clusters of S. clavuligerus and N. lactamdurans. Availability of the cloned genes allows metabolic engineering of the β-lactam biosynthetic pathways such as a channelling precursors and directed removal of bottlenecks in the β-lactam biosynthetic pathways. Several new β-lactam antibiotics have been discovered in gram-positive and gram-negative bacteria that will provide new genes for combinatorial synthesis of new molecules. Received: 2 December 1997 / Received revision: 20 February 1998 / Accepted: 24 February 1998     

The genus Amycolatopsis: Indigenous plasmids, cloning vectors and gene transfer systems

The genus Amycolatopsis is a member of the phylogenetic group nocardioform actinomycetes. Most of the members of the genus Amycolatopsis are known to produce antibiotics. Additionally, members of this genus have been reported to metabolize aromatic compounds as the sole sources of carbon and energy. Development of genetic manipulation in Amycolatopsis has progressed slowly due to paucity of genetic tools and methods. The occurrence of indigenous plasmids in different species of Amycolatopsis is not very common. Till date, only three indigenous plasmids viz., pMEA100, pMEA300 and pA387 have been reported in Amycolatopsis species. Various vectors based on the indigenous plasmids, pMEA100, pMEA300 and pA387, have been constructed. These vectors have proved useful for molecular genetics studies of actinomycetes. Molecular genetic work with Amycolatopsis strains is not easy, since transformation methods have to be developed, or at least optimized, for each particular strain. Nonetheless, methods for efficient transformation (polyethyleneglycol (PEG) induced protoplast transformation, transformation by electroporation and direct transformation) have been developed and used successfully for the introduction of DNA into several Amycolatopsis species. The construction of plasmid cloning vectors and the development of gene transfer systems has opened up possibilities for studying the molecular genetics of these bacteria.     

Assessing population genetic structure via the maximisation of genetic distance

Background

The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics.

Methods

In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set.

Results

The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for F_ST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for F_ST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found.

Conclusion

This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present.     

Towards genetic improvement of commercially important microalga Haematococcus pluvialis for biotech applications

Haematococcus pluvialis is a unicellular green alga which produces a ketocarotenoid, astaxanthin which has pharmaceutical and nutraceutical applications owing to its high antioxidant activity. Biotechnological approaches such as genetic transformation methods (Agrobacterium-mediated) and cloning strategies, are essential to improve/regulate this ketocarotenoid in Haematococcus. For this studies are necessary to improve Haematococcus through biotechnological means. In this connection, a suitable cocultivation medium for Haematococcus and Agrobacterium tumefaciens was standardized and different antibiotics were screened. Among the cocultivation media viz Z₈, Bold’s Basal Medium, Tris Acetate Phosphate Z₈ with 0.5% mannitol and BBM and Z₈ with half strength LB TAP medium was found suitable for growth of both the alga Haematococcus and Agrobacterium. For the different antibiotics screened to identify the sensitivity of algae, hygromycin at more than 2 mg L⁻¹ showed lethal effect which can be used as a selectable marker gene in genetic transformation, whereas cefotaxime and augmentin showed no effect up to 2,000 mg L⁻¹. The growth of algae was higher in solid selection medium when compared to the liquid selection medium.     

Microsatellite variation in Bavarian populations of European grayling (Thymallus thymallus): Implications for conservation

European grayling populations in Bavaria have shown steady declines during the last 10–20years. In order to provide guidelines for conservation strategies and future management programs, we investigated the genetic structure of 15 grayling populations originating from three major Central European drainages (the Danube, the Elbe and the Rhine/Main) using 20 microsatellite loci. Genetic divergence between the three drainage systems was substantial as illustrated by highly significant heterogeneity of genotype frequencies, high number of drainage-specific private alleles, high between-drainage F _ST values, high assignment success of individuals to their drainage of origin and the high bootstrap support for the genetic distance based drainage-specific population clusters. In agreement with earlier studies, microsatellites revealed relatively low levels of intrapopulational genetic diversity in comparison to the overall level of variation across populations. Maximum likelihood methods using the coalescent approach revealed that the proportion of common ancestors was generally high in native populations and that the estimates of N _e were correlated with the genetic diversity parameters in all drainages. The number of effective immigrants per generation (N _e m) was less than one for all pairwise comparisons of populations within the drainages, indicating restricted interpopulational gene flow. Based on these findings we recommend a drainage and sub-drainage specific conservation of grayling populations in order to preserve their overall genetic diversity and integrity. For large-scale stocking actions to supplement declining or to restore extinct populations, creation of separate broodstocks for major conservation units (ESUs and MUs) is warranted. This revised version was published online in July 2006 with corrections to the Cover Date.     

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger’s agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976–2003). Global genetic differentiation between the two collections was very low (F _st = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F _st, and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers’ management has globally preserved sorghum genetic diversity in Niger.