Genetic relationship of mungbean and blackgram genotypes based on agronomic and photosynthetic performance and SRAP markers

Genetic identification is at the base of parental selection in varietal development programs. Agronomic and photosynthetic characters and sequence-related amplified polymorphism (SRAP) markers were analyzed for two legume species which included 23 mungbean (Vigna radiata (L.) Wilczek) and four blackgram (Vigna mungo (L.) Hepper) genotypes. The results revealed that the seeds/pod, plant height, pods/plant, pod length, days to flowering, and all photosynthetic characters studied had a significant correlation with the yield/plant. Using UPGMA analysis with phenotypic data, five clusters and two individuals were identified. Twenty-five SRAP primer combinations generated 562 amplified bands, of which 507 were polymorphic (90.2%). The average numbers of scorable and polymorphic bands/primer pair were 22 and 20, respectively. Two major clusters coincided with two species having a 100% bootstrap value. Within the mungbean cluster, there were two subclusters containing 12 and 11 mungbean genotypes. Mantel’s test demonstrated that the polymorphisms given by SRAPs were associated with agronomic and photosynthetic variability (r = 0.734, p < 0.01). These results allow promising mungbean genotypes to be identified through genetic diversity and field performance which can be utilized as potential parents towards future breeding programs. Moreover, the factors which contribute most to yield/plant can be simultaneously used as selection criteria for yield improvement.

Analysis of genetic diversity in Elytrigia repens germplasm using intersimple sequence repeat (ISSR) markers

The genetic diversity among 30 accessions of Elytrigia repens (L.) Nevski was analyzed using 100 intersimple sequence repeat (ISSR) primers, 12 of which generated distinct amplification products. Out of the 132 repeatable bands detected, 100 bands were polymorphic. The percentage of polymorphic bands was 70.66%, with a mean of 8.33 percentage of polymorphic bands per primer. The ISSR-based genetic similarity coefficients among the 30 accessions ranged from 0.509 to 0.873, revealing high genetic diversity. The 30 E. repens accessions were divided into eight groups based on an unweighted pair-group method with arithmetic mean cluster analysis and a principal components analysis. We found that genetic distance is correlated with geographical distance among the 30 E. repens accessions studied (r = 0.812, p < 0.05) using Mantel’s test. Our results confirm the potential value of genetic diversity preservation for future breeding programs.

Identification of the Polish strains of Chalara ovoidea using RAPD molecular markers

On the basis of morphological features and RAPD markers the strains of <em>Chalara ovoidea</em> found in Poland on planks and on stems of beech trees were identified. As reference strains the cultures taken from CBS Utrecht were employed; they were cultures CBS 354.76 and CBS 136.88. The amplification of genomic DNA was conducted using 10 primers (OPA01-OPA10), 7 of which (OPA01-OPA05, OPA09, OPA10) gave positive results. In total 42 fragment of DNA (bands) were obtained. In case of primers OPA03, OPA04, OPA05, and OPA09 all obtained fragments for analyzed strains were fully monomorphic. This means, that no genetic variability was found using the above mentioned primers. Low genetic variability was ascertained in the analysis of frequency of occurrence of DNA fragments using other primers, namely OPA01, OPA02, and OPA10. The matrix and dendrogram of genetic affinities among different strains of <em>Chalara</em>, calculated using the Jaccard’s similarity coefficient suggested, that the most similar strains are the ones coming from Poland (HMIPC 16136 and HMIPC16664) as well as the strain CBS 136.88, while somewhat different from them is the strain CBS 354.76. To determine, how exactly did the dendrogram reflect genetic affinity among analyzed strains, the Mantel’s test was employed. The correlation coefficient amounted to 0.78, suggesting that the strains under study had been grouped properly. The results showed, that the fungal strains found in southern Poland represent the species Chalara ovoidea.

Development and utilisation of conserved-intron scanning marker in sugarcane

Genetic dissection of economic traits in sugarcane requires sufficiently informative molecular markers that are currently lacking in this highly valued crop. Through comparative analysis of publicly available expressed-sequence data of sugarcane, sorghum and barley, and the whole rice genome-sequence survey, novel functional markers based on conserved-intron scanning primers (CISP) were developed and evaluated in different accessions across various taxonomic ranks of sugarcane. Polymorphism was moderate (55.2%), whereas 94.7% of the markers developed amplified fragments in selected genotypes. Mean polymorphism information content value was 0.582 (range 0.320–0.715), which was comparable to that with genic microsatellite markers (0.52) but lower than that with EST-SSR (0.73). Genetic-similarity coefficient ranged from 0.39 to 0.95, indicating variable levels of divergence depending on the taxonomic rank assessed. Cluster analysis revealed that the genotypes grouped in accordance with the taxonomical classification of sugarcane, with a relatively good support from a Mantel’s test (r = 0.847) and a moderate bootstrap value (65–89%). The CISP markers reported in the present study have potential utility for genetic-diversity analysis and application in sugarcane-breeding programs.

Extent and pattern of genetic differentiation within and between phenotypic populations of Leymus chinensis (Poaceae) revealed by AFLP analysis

The extent and pattern of genetic differentiation between two naturally occurring phenotypes, grey–green leaf (GGL) and yellow–green leaf (YGL), of Leymus chinensis (Trin.) Tzvel., which colonize distinct habitats in the Songnen Prairie in northeast China, were investigated by amplified fragment length polymorphism (AFLP) analysis. Twelve selected AFLP primer pairs amplified 593 reproducible bands, of which 148 (24.96%) were polymorphic among 69 individuals taken from three populations: two natural ones (YGL and GGL1) and one transplanted (GGL2). Cluster analysis based on the AFLP data categorized the plants into distinct groups that are in line with their phenotypes and population origins, thus denoting clear genetic differentiation between the two phenotypes. This, together with their adaptation to contrasting natural habitats, suggests that the two phenotypes probably represent stabilized ecotypes. The grouping was supported by multiple statistical analyses including Mantel’s test, principal coordinate analysis (PCOORDA), and analysis of molecular variance (AMOVA). The GGL phenotype harbors a higher level of within-population genetic diversity than YGL, possibly reflecting selection by habitat heterogeneity. Although GGL2 is largely similar to its original population (GGL1), further diversification since transplantation was evident. Sequence analysis of a subset of phenotype-specific or phenotype-enriched AFLP bands implicated diverse biological functions being involved in ecological adaptation and formation of the two phenotypes.

Falconiformes assemblages in a fragmented landscape of the Atlantic Forest in Southern Brazil

An ecological analysis focused on distribution of Falconiformes, comprising abundance and morphology data, is provided. Samples were collected in a fragmented landscape within the Atlantic Rainforest, southern Brazil, between August and November 2001. Four main types of habitats were pinpointed among the 30 different sampling sites, while eight external morphological traits were employed. Twenty-one Falconiformes species were detected and jackknife estimates for regional richness reached 24.8 ± 2.56 species (p<0.05). There were no differences between average number of diurnal birds of prey species in the different habitats under analysis (H-test, p>0.05). Mantel's test for relative abundance and species morphology reveals weak association rates, corroborating the lack of association between matrixes (r = 0.059, p>0.05). Difficulties in the analyses of distribution and species morphology data may have been caused by their generalist character and may be due to the high rate of environment degradation revealed by the regional landscape's mosaic aspect.

Identification of Metalliferous Ecotypes of Cistus ladanifer L. using RAPD Markers

The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel’s test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures.

Specific genetic markers for wheat, spelt, and four wild relatives: comparison of isozymes, RAPDs, and wheat microsatellites

Three types of markers—isozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatellites—were tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites.Key words: Triticeae, isozymes, RAPDs, microsatellites, polymorphism.