Genetic variation within a fragmented population of swietenia humilis zucc

With large tracts of once continuous forest now modified by human use to leave reduced and highly fragmented stands of trees, the determination of the genetic consequences of forest fragmentation is a priority for ascertaining the conservation value of resultant stands, and in formulating sustainable management strategies. The levels and distribution of genetic diversity over 10 microsatellite loci were investigated within a fragmented population of the neotropical tree Swietenia humilis Zucc. High levels of genetic variation, typical of a highly outcrossing species, were found in all fragments at all loci (mean HE = 0.548). The majority of the variation was within rather than between fragments (RST = 0.032), giving high indirect estimates of gene flow (Nm = 8.9), probably reflecting the genetic structure of the trees present under more continuous forest. A high proportion of loci also showed significant departures from Hardy-Weinberg equilibrium with associated significant levels of FIS. The initial effects of fragmentation were, however, seen in the fragments through the loss of low-frequency alleles present in the continuous 'control' stand. The percentage of this allelic loss increased with a decrease in fragment size.

A low mutation rate for chloroplast microsatellites

We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3. 2 x 10(-5) and 7.9 x 10(-5). This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

Copia-SSR: A simple marker technique which can be used on total genomic DNA

We have developed a PCR-based assay which uses a combination of two classes of repetitive elements found in eukaryotic genomes, namely Ty1-Copia retrotransposons and simple sequence repeats, to amplify multiple polymorphic products from total genomic DNA. Using the technique, seven markers were mapped to four different chromosome arms using a barley doubled haploid mapping population. This technique offers a simple and efficient method of generating both dominant and codominant genetic markers in virtually any eukaryote for mapping and diversity studies.Key words: Copia-SSR, microsatellite, retrotransposon, barley, genotyping.

Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam

Moringa oleifera is an important multipurpose tree introduced to Africa from India at the turn of this century. Despite limited knowledge of the levels of genetic diversity and relatedness of introduced populations, their utilization as a source of seed for planting is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for a selective breeding programme, genetic analysis of seven populations was performed using amplified fragment length polymorphism (AFLP) markers. The four pairs of AFLP primers (PstI/MseI) generated a total of 236 amplification products of which 157 (66.5%) were polymorphic between or within populations. Analysis of molecular variance (AMOVA) revealed significant differences between regions and populations, even though outcrossing perennial plants are expected to maintain most variation within populations. A phenetic tree illustrating relationships between populations suggested at least two sources of germplasm introductions of Kenya. The high levels of population differentiation detected suggest that provenance source is an important factor in the conservation and exploitation of M. oleifera genetic resources.

Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum

In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum, which includes cultivated barley (H. vulgare ssp. vulgare) and its wild progenitor H. vulgare ssp. spontaneum. Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many corp species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.

An example of microsatellite length variation in the mitochondrial genome of conifers

In the present study, the intergenic region between the mitochondrial genes encoding subunit 3 of NADH dehydrogenase (nad3) and ribosomal protein S12 (rps12) was shown to contain a Gn mononucleotide microsatellite repeat. This region was analysed in 15 species belonging to the genus Pinus and interspecific variation was detected in the form of repeat length polymorphism. Sequence analysis of a 576-bp region containing the microsatellite confirmed that the variability was due to expansion and contraction of the repeat motif and that no point mutations were present in the coding regions of the two genes. This is the first report of the occurrence of a microsatellite polymorphism in plant mitochondria.Key words: mitochondrial, microsatellite, Pinus, hard pines, taxonomy.

Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley

Simple sequence repeat (SSR)-based genetic markers are being actively developed for the majority of crop plant species. In barley, characterization of 290 dinucleotide repeat-containing clones from SSR-enriched libraries has revealed that a high percentage are associated with cereal retrotransposon-like and other dispersed repetitive elements. Associations found were with BARE-1, WIS2-1A, PREM1 and the dispersed repetitive element R173. Additional similarities between different SSR clones, which have no matches in DNA sequence databases, indicate that this phenomenon is probably widespread in the barley genome. Sequence homologies to the non-coding regions of several cereal genes were also explained by homology to mobile genetic elements. The SSRs found can therefore be classified into two types: (1) those with unique sequences on either flank, and (2) those which are intimately associated with retro-transposons and other dispersed repetitive elements. As the cereal genome is thought to consist largely of this type of DNA, some random association would be expected. However, the conserved positions of the SSRs, relative to repetitive elements, indicate that they have arisen non-randomly. Furthermore, this class of SSRs can be classified into three subtypes: (1) those which are positioned 3' of a transposable element with unique sequence on the other flank, (2) those positioned 5' of a transposable element, and (3) those which have arisen from an internal sequence and so have transposable element sequence on both flanks. The first appear to be analogous to the class of SSRs in mammalian systems which are associated with Alu elements and SINEs (short interspersed elements) and which have been postulated to arise following integration of an extended and polyadenylated retro-transcript into the host genome, followed by mutation of the poly(A) tract and expansion into an SSR. For the second, we postulate that a proto-SSR (A-rich sequence) has acted as a 'landing pad' for transposable element insertion (rather than being the result of insertion), while the third includes those which have evolved as a component of an active transposable element which has spread throughout the genome during bursts of transposition activity. The implications of these associations for genome and SSR evolution in barley are discussed.

An example of microsatellite length variation in the mitochondrial genome of conifers

In the present study, the intergenic region between the mitochondrial genes encoding subunit 3 of NADH dehydrogenase (nad3) and ribosomal protein S12 (rps12) was shown to contain a Gn mononucleotide microsatellite repeat. This region was analysed in 15 species belonging to the genus Pinus and interspecific variation was detected in the form of repeat length polymorphism. Sequence analysis of a 576-bp region containing the microsatellite confirmed that the variability was due to expansion and contraction of the repeat motif and that no point mutations were present in the coding regions of the two genes. This is the first report of the occurrence of a microsatellite polymorphism in plant mitochondria.

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.

Evaluating genetic relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri Lanka by means of AFLP profiling

PCR-based DNA profiling of coconut palms indigenous to Sri Lanka was conducted using amplified fragment length polymorphism (AFLPs). A total of 322 amplification products were generated from the 42 genotypes with eight pairs of primers (EcoRI and MseI). Overall most variation was detected in the tall (Typica) rather than the intermediate (Aurantiaca) and dwarf (Nana) forms. A hierarchical analysis of molecular variance (AMOVA) was used to quantify and partition levels of variability into between- and within-form components. This revealed that for the inbreeding dwarf and intermediate forms most variation was observed between, rather than within, forms. In contrast, the outbreeding tall forms exhibited as much variation within as between forms. These observations have important implications for the maintenance and collection of coconut germplasm. This study also provided insights into the genetic (as opposed to phenotypic) relatedness of coconut accessions. Morphologically the Aurantiaca group of accessions are considered to be intermediate between the tall and dwarf accessions. Estimation of genetic relatedness based on AFLP analysis identified the Aurantiaca group as being more similar to the dwarf rather than the tall group. In addition, putative duplicate accessions were identified in the Aurantiaca group. Information emerging from this study will facilitate the management of coconut germplasm and optimise the choice of genetically divergent parents for crossing.

Effect of two obturation techniques on the filling of lateral canals and the main canal

The three-dimensional obturation of the root canal system is widely accepted as a key factor for successful endodontic therapy. The purpose of this study was to evaluate the obturation of lateral canals and the main canal using cold lateral condensation versus the gutta-percha coated rigid carrier. Thirty epoxy blocks with five lateral canals placed at varying angles from the main canal were used. Each experimental group was obturated by a board certified endodontist with clinical experience in the respective obturation technique. The length of gutta-percha and sealer in the lateral canals was measured under a microscope (x30, Unitron) to the nearest 0.5 mm. The blocks were sectioned with an Isomet Plus precision saw (Buehler, Lake Bluff, IL) and copious water irrigation perpendicular to the main canal at the apex, the height of contour, and at 0.8, 1.6 and 2.4 mm from the canal apex. A microscope (x100, Leitz, Switzerland) was used to determine voids. There was significantly (p < .001) more gutta-percha in the lateral canals with the gutta-percha coated rigid carrier technique. In contrast, the cold lateral condensation technique had significantly (p < .001) more sealer in the lateral canals. However, there was no significant (p < .05) difference, in gutta-percha-plus-sealer filling of the lateral canals, between the two techniques. In the apical 1 mm of the main canal there were significantly (p < .011) fewer voids with the gutta-percha coated rigid carrier technique compared to the cold lateral condensation. In the model chosen, the gutta-percha coated rigid carrier technique and the cold lateral condensation technique were equally effective in filling lateral canals. In filling the main canal, however, the coated rigid carrier technique was more effective.

Discriminating between barley genotypes using microsatellite markers

Eleven microsatellite loci were used to survey 24 barley genotypes representing 23 cultivars and a breeding line in official trials. Three separate combinations of four microsatellites had overall probabilities of identity of less than 1 in 1000 and could distinguish between all 24 barley genotypes. It is shown that the microsatellites could distinguish genotypes with the same pedigree and also that patterns of discrimination were different from those obtained from botanical descriptors. The stability of microsatellites across different generations was demonstrated by a retrospective analysis of the pedigree of Golden Promise. One of the parents of Maythorpe, the immediate ancestor of Golden Promise, was shown to be Irish Goldthorpe rather than Goldthorpe, thereby resolving conflicting published pedigrees.

Homology of AFLP products in three mapping populations of barley

Segregation of 850 polymorphic AFLP (amplified fragment length polymorphism) fragments was followed in three different doubled haploid (DH) barley populations, Dicktoo x Morex (DM), Igri x Franka (IF) and Blenheim x E224/3 (BE), which had previously been used to construct linkage maps using other molecular markers. The final maps consisted of 310, 655 and 474 markers, of which 234, 194 and 376, respectively, were AFLPs. A comparison of profiles from the parental lines identified 51 similar-sized AFLPs segregating in both DM and IF populations, 20 in the DM and BE populations and 18 in the IF and BE populations. Eight segregated in all three. Analysis of the complete datasets for each of the populations using Joinmap V.2. indicated that in general terms each of the AFLPs which were polymorphic in more than one population mapped to the same genetic locus. The number of co-dominant markers segregating in a single population ranged from 6% for DM to 12.6% for IF. These results are discussed in the context of using AFLP in genetic linkage and diversity studies.

AFLP variation in wild barley (Hordeum spontaneum C. Koch) with reference to salt tolerance and associated ecogeography

Thirty-nine genotypes of Hordeum spontaneum were selected from three geographically separated areas (southwestern, northern, and southeastern) of the Fertile Crescent. The lines were subject to AFLP (amplified fragment length polymorphism) analysis from which a similarity matrix was produced. A dendrogram of the data showed, with two exceptions, that the genotypes grouped together according to area of origin. This was confirmed by principal coordinate analysis in which the first principal coordinate separated the genotypes of the southwestern area from the other two areas, which in turn could be separated by the second principal coordinate. While genotypes from the same site of origin can exhibit very similar AFLP profiles, sharp genetic differences were detected between genotypes separated by relatively short distances. Thirty of the 39 genotypes were subjected to hydroculture salt tolerance tests. These were analysed for shoot Na+ content and carbon isotope composition (δ13C) after 4 weeks of treatment (100 mol∙m−3 NaCl). Shoot Na+ content and δ13C were highly correlated. Twelve AFLP markers were found to be associated with both shoot Na+ content and shoot δ13C and were also associated with site of origin ecogeographic data, particularly longitude. The most salt tolerant genotype came from Ilam in the southeastern area and the most salt sensitive genotype originated in the southwestern area. The 12 markers were partitioned into groups that showed significant associations within groups but no significant association between groups. In a multiple regression analysis, three AFLP markers, from separate groups, accounted for more than 60% of the variation for shoot Na+ content and δ13C. The results demonstrate the effectiveness of AFLP fingerprinting in genetic studies of complex traits at the wild species and (or) population level.Key words: wild barley, Hordeum spontaneum, AFLP, salt tolerance.

Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP)

Retrotransposons are present in high copy number in many plant genomes. They show a considerable degree of sequence heterogeneity and insertional polymorphism, both within and between species. We describe here a polymerase chain reaction (PCR)-based method which exploits this polymorphism for the generation of molecular markers in barley. The method produces amplified fragments containing a Bare-1-like retrotransposon long terminal repeat (LTR) sequence at one end and a flanking host restriction site at the other. The level of polymorphism is higher than that revealed by amplified fragment length polymorphism (AFLP) in barley. Segregation data for 55 fragments, which were polymorphic in a doubled haploid barley population, were analysed alongside an existing framework of some 400 other markers. The markers showed a widespread distribution over the seven linkage groups, which is consistent with the distribution of the Bare-1 class of retrotransposons in the barley genome based on in situ hybridisation data. The potential applicability of this method to the mapping of other multicopy sequences in plants is discussed.