Morphological and molecular diversity among Italian populations of Quercus petraea (Fagaceae)

Quercus petraea (sessile oak) has a scattered distribution in southern and central Italy. The objective of this work was to evaluate the level and distribution of diversity in five Italian populations of Q. petraea by using morphological markers and hypervariable molecular markers such as microsatellites. Forty-eight morphological traits and six nuclear and three plastid loci were scored for each population. Evidence for differentiation in both sets of traits was found, but patterns of differentiation of morphological traits did not coincide with microsatellite differentiation. Morphological variation was correlated with ecological conditions at the site of origin. Analysis of molecular variance revealed significant genetic variation among populations (P < 0.001), both at the nuclear and plastid levels. There was a slight, but significant, correlation between nuclear genetic distance and geographic distance. The relatively high genetic diversity in the populations analysed indicates that the maintenance of their evolutionary potential is possible if population sizes are maintained or increased. Low levels of haplotype diversity found within the small southernmost population (Piano Costantino) indicates that genetic erosion may increase the extinction risk for this population.     

Genetic diversity assessment of summer squash landraces using molecular markers

Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash.     

Genetic variability among sorghum accessions from the Sahelian agroecological region of Burkina Faso

The authors collected Sahelian sorghum landraces of Burkina Faso in 1984 and 74 of these accessions were characterized in 1985–1986 at Gampela in Burkina Faso (West Africa). The five races of cultivated sorghum were represented in this zone but 63.5% of the accessions were Guinea type. Great intra-and inter-accession variability was found. Plants were tall and had long panicles and small to intermediate seeds. There was a strong association between days-to-flowering, number of internodes, panicle length and height. The 100-kernel weight showed an antagonism with days to flowering and tillering. Multivariate analyses were made which enabled the accessions to be classified into four groups. The group most adapted to the sahelian zone, sahelian group, was semi-late, developed intermediate size of vegetative organs, had moderate tillering and had the best yield per plant.     

Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers’ perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F _is over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F _st = 0.36). Historical factors, variation in breeding systems, and farmers’ practices all affected patterns of genetic variation. Farmers’ practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.     

Morphological variability within Oesophagostomum bifurcum among different primate species from Ghana

Adult Oesophagostomum bifurcum (Nematoda: Strongylida) from human and non-human primates from Ghana were compared in order to investigate the extent of morphological variability within the species. Using analysis of variance and principal component analysis, significant differences in morphological characters (such as parasite length, width, length of the oesophagus and length of spicules) were demonstrated between O. bifurcum worms from humans, the Mona, Patas or Green monkey and/or Olive baboons. These findings suggest that O. bifurcum from different species of primate host represent distinct population variants, also supported by recent epidemiological and genetic studies of O. bifurcum from such hosts.     

Assessment of genetic diversity among sorghum landraces and their wild/weedy relatives in western Kenya using simple sequence repeat (SSR) markers

Understanding the extent of gene exchange between cultivated sorghum and its wild/weedy relatives and the evolutionary processes (including farmers’ practices) that act to shape the structure of genetic diversity within and between them is an important aspect for germplasm conservation strategies, biosafety risk assessment, and crop improvement programs. In this study, molecular characterization and genetic diversity analyses were conducted on wild, weedy and cultivated sorghums collected at a local-scale in a traditional farming system in the Lambwe Valley of western Kenya. Nine simple sequence repeat (SSR) markers were used to genotype 294 cultivated sorghum and 200 wild sorghum individuals. The nine SSR markers were highly polymorphic with a number of alleles that varied from 2 to 19. Overall, wild sorghums had higher genetic diversity, observed heterozygosity, total number of alleles, polymorphic information content and more genotypes per locus than the cultivated types. A Mantel test demonstrated that there was significant isolation-by-distance for wilds and cultivated materials. STRUCTURE, cluster and principal coordinate analyses consistently assigned wild and cultivated individuals to different groups but failed to place hybrids/weedy types as a single separate group from wilds. Our results provide strong evidence of significant genetic diversity retained within wilds, larger divergence between wild and cultivated materials and reduced gene flow than those previously reported in Kenya. These results demonstrate the value of the Lambwe Valley region as a genetic reservoir and the importance to conduct genetic diversity studies at the local scale to design and execute appropriate in situ conservation programs and policies.     

Genomic diversity among sorghum genotypes with resistance to sorghum shoot fly, Atherigona soccata

Host plant resistance is one of the important components for management of sorghum shoot fly, Atherigona soccata. The levels of resistance in cultivated germplasm are low to moderate, and therefore, it is important to identify sorghum genotypes with diverse mechanisms of resistance based on physico-chemical and or molecular markers. We assessed the genetic diversity of 15 sorghum genotypes with different levels of resistance/susceptibility to shoot fly, A. soccata using 93 sorghum simple sequence repeat (SSR) primer pairs and simultaneously characterized for 15 morpho-biochemical traits associated with shoot fly resistance. Of these 93 SSR primer pairs, amplification products from 79, thought to correspond to single-copy loci distributed across all ten sorghum chromosome pairs, showed good polymorphism across the 15 sorghum genotypes. The polymorphic information content (PIC) values of these 79 SSR markers ranged from 0.06 to 0.86. The Principal Coordinate Analyses (PCoA) and cluster analyses based on dissimilarity matrices derived from SSR based allelic variation (Neighbor-Joining distance) and variation in 15 morpho-biochemical traits (based on Gower??s distance), revealed grouping of most susceptible genotypes in single cluster. The improved breeding lines grouped with resistant or susceptible genotypes, based on shared pedigree. Based on these results, three resistant accessions viz., IS 1054, IS 1057 and IS 4664 were found diverse to IS 18551, which is widely used as shoot fly resistance donor. These diverse sources, after further characterization for resistance mechanisms, can be used in breeding programs for improving shoot fly resistance.     

Morphological and molecular characterization of Calothrix isolates obtained from diverse environments in India

Abstract-Thirty cyanobacterial strains of Calothrix (family Rivulariaceae) isolated from diverse geographical regions of India were analyzed using morphological and molecular approaches. Most of the isolates were planktonic while some grew benthically. Significant differences were observed with regard to the shape and size of the vegetative cells, heterocysts, and akinetes. Analyses of molecular polymorphisms using Restriction Fragment Length Polymorphisms (RFLP) of 16S rRNA genes with the reference strain led to unambiguous differentiation of the isolates as well as understanding of their genetic relationships.     

Analysis of phenotypic and microsatellite-based diversity of maize landraces in India,especially from the North East Himalayan region

The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize landrace accessions, including the ‘Sikkim Primitives’ which have a unique habit of prolificacy (5–9 ears on a single stalk). Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic characters clearly separated ‘Sikkim Primitives’ from the rest of the accessions. PCA revealed two principal components describing 90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence repeat (SSR) markers using a ‘population bulk DNA fingerprinting strategy’, with allele resolution using an automated DNA Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content (PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions. Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies ≥0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits, indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers’ genetic distance also revealed distinct genetic identity of the ‘Sikkim Primitives’ from the rest of the accessions in India, including Sikkim. Mantel’s test revealed significant and positive correlation between the phenotypic and molecular genetic dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize landraces from the NEH region in India.     

Genetic variation among pumpkin landraces based on seed qualities and molecular markers

Molecular Biology Reports - Germplasm identification is an essential connection linking the conservation and exploitation of crop genetic resources in several plant breeding programs. This study...     

Morphological and molecular diversity among populations of Quercus brantii Lindl. in western forest of Iran

Abstract

This study represents a preliminary step toward understanding the genetic structure of Persian oak in Iran. The genetic variability of Quercus brantii in Western forest of Iran was evaluated by amplified fragment length polymorphism (AFLP), chloroplast microsatellite and leaf morphology. Fifty-five trees from eight regions were sampled from across the range of Chaharmahal va Bakhtiari province of Iran. Twenty morphological traits were analyzed through clustering and ordination method. At morphological level, the applied statistics suggest that macromorphological traits significantly differentiate between populations. The overall sample shows a proportion of AFLP polymorphic markers of 92.1%, denoting a high level of variability. Based on AFLP data, differences among populations within geographic regions account for 11.6% of the total variation and only 0.57% is attributed to variation among regions. Based on chloroplast microsatellite (cpSSR), 34% of total variation was found among populations, suggesting a high within-population haplotype diversity. The dendrogram obtained from cpSSR showed a general pattern quite different from the pattern obtained from morphological analysis and AFLP markers.     

Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers

 The level of genetic diversity and the population genetic structure of sorghum landraces from North-western Morocco have been investigated based on direct field-sampling using both allozyme and microsatellite markers. As expected, microsatellite markers showed a much higher degree of polymorphism than allozymes, but relative measures of genetic structure such as Wright’s inbreeding coefficient F _IS and Nei’s coefficient of genetic differentiation G _ST were similar for the two sets of markers. Substantial inbreeding was found to occur within fields, which confirms that sorghum is predominantly selfing under cultivation. Most of the genetic diversity in Moroccan landraces occurs within fields (more than 85%), as opposed to among fields or among regions, a result which contrasts to those of studies based on accessions from germplasm collections. It is suggested that individual fields of sorghum constitute valuable units of conservation in the context of in situ conservation practices. Received: 8 December 1998 / Accepted: 28 December 1998     

Morphological variability in Rhizoctonia solani isolates from different agro-ecological zones of West Bengal,India

Sheath blight caused by Rhizoctonia solani Kühn is one of the most important diseases of rice, resulting in significant yield loss in rice every year. The rice-based intensified cropping system, edapho-climatological and host variations make the disease problem more complicated. However, the incidence and severity of the disease differ from one location to other, one geographical area to other and even differs from country and region wise. The reasons for this disease severity have been attributed to the variation in host genotype, virulence of the pathogen, prevalence of congenial soil physico-chemical and plants’ surrounding environment and cultural practices. Sixty-seven number of isolates of R. solani from rice, 12 no. of R. solani isolates associated with maize, sugarcane, weeds, cabbage, pointed gourd, watermelon, potato, dolichos bean and aparajita were isolated from different agro-ecological region of West Bengal and three no. of isolates of R. oryzae-sativae obtained from Department of Plant Pathology, BCKV, were used in the present study. Cultural and morphological characteristics revealed considerable diversity among the R. solani isolates. Cultural and morphological analysis of WB isolates of rice has indicated that the diversity among the isolates does not correlated with their origin. On the basis of morphological characteristics, R. solani isolates could be easily separated from R. oryzae-sativae isolates. The no. of sclerotia, hyphal length, wt. of sclerotia and mycelial growth rate are the important morphological markers for differentiation of R. oryzae-sativae from R. solani isolates.     

采自东南亚的变色卧孔菌一新种（英文）

报道了采自新加坡的多孔菌一新种,硫色变色卧孔菌,并对该种进行了描述和显微绘图。该种的主要特征是子实体一年生,平伏,新鲜时软,硫磺色,干后浅橄榄色至蜜黄色,单系菌丝系统,生殖菌丝具简单分隔,存在菌丝状囊状体和锥形拟囊状体,担孢子近球形至球形,具一大液泡。基于ITS和LSU序列的系统发育分析表明该新种属于变色卧孔菌属分支的一个明确的支系。     

Morphological variability and molecular phylogeny of the nematophagous fungus Monacrosporium drechsleri

An isolate of the nematode-trapping fungus Monacrosporium drechsleri was collected from cultures of the root-knot nematode Meloidogyne arenaria that had been maintained on tomato roots in greenhouse pots in Beltsville, Maryland. The plant-parasitic nematodes Heterodera glycines, Meloidogyne incognita and Pratylenchus zeae and the free-living nematodes Caenorhabditis elegans and Panagrellus redivivus were placed on colonies of M. drechsleri grown in Petri dishes to study ability of the isolate to trap various nematode hosts. None of the nematodes placed near adhesive knobs were motile within 1 d. To determine where M. drechsleri fits within the existing phylogeny of nematode-trapping fungi, the ITS1-ITS2 regions of rDNA and the nuclear gene EF1-alpha were sequenced for the new isolate of M. drechsleri, for the species M. parvicolle and M. lysipagum, and for an isolate of M. ellipsosporum distinct from the one listed in GenBank. Parsimony trees were constructed showing the closest molecular relative of M. drechsleri to be the newly sequenced isolate of M. ellipsosporum; the latter had a highly divergent sequence from the sequence recorded in GenBank for a different isolate of M. ellipsosporum. Unique, consistent and discrete morphological characters are absent in these related taxa, so an independent molecular character should be considered essential for their accurate identification.     

Novel primers reveal wider diversity among marine aerobic anoxygenic phototrophs

Aerobic anoxygenic phototrophic bacteria (AAnPs) were previously proposed to account for up to 11% of marine bacterioplankton and to potentially have great ecological importance in the world's oceans. Our data show that previously used primers based on the M subunit of anoxygenic photosynthetic reaction center genes (pufM) do not comprehensively identify the diversity of AAnPs in the ocean. We have designed and tested a new set of pufM-specific primers and revealed several new AAnP variants in environmental DNA samples and genomic libraries.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.     

Genetic diversity in maize landraces from indigenous settlements of Northeastern Argentina

In South America, native maize germplasm has been extensively studied particularly for the Andean region. However, relatively few genetic diversity studies include materials from the eastern region of the continent. Herein we present a genetic diversity characterization of four Popcorn maize landraces, maintained in indigenous settlements, from Northeastern Argentina (NEA). In addition, one Popcorn landrace from Northwestern Argentina (NWA) was incorporated for comparison. We characterized these landraces using ten microsatellite markers. For the whole data set, a total of 65 alleles were found, with an average of 7.22 alleles per locus. The average gene diversity was 0.370. Global fit to Hardy–Weinberg proportions was observed in all landraces. Global estimates of F _ST revealed a significant differentiation among the populations. Individual Neighbor-joining clustering and Bayesian analyses allowed the recognition of most populations studied. Two main groups were distinguished by the Neighbor-joining clustering of populations. This grouping pattern would be consistent with a hypothesis of successive introductions of Popcorn in South America. The results presented will be useful to design strategies that maximize the utility of maize genetic resources.