Genetic characterization of Libyan date palm resources by microsatellite markers.

Molecular typing of 377 female date palm trees belonging to 18 Libyan cultivars and representing common genotypes in the central Libyan oasis of Al Jufrah was performed using 16 highly polymorphic microsatellite or SSR loci. A total of 110 alleles with an average of 6.88 alleles per locus were scored indicating the high level of polymorphism existing among the cultivars thus allowing their genetic fingerprinting. Moreover 28 alleles out of 110 were fixed. All the cultivars were characterized by negative values of the Fixation Index (F) due to an excess of heterozygotes with respect to HW equilibrium. The pattern of genetic diversity among cultivars was estimated by codominant genetic distances and presented by principal coordinates analysis (PCoA). The observed pattern evidences the genetic diversity existing among cultivars that allow distinguishing them easily. The average dissimilarity internal to each cultivar ranged from 0 to 21. Seven cultivars showed value zero indicating no genetic difference within cultivar in agreement with their Fixation Index (F = 1). A varietal identification key was also built using multiloci genotyping with only three microsatellite loci that identified 23 alleles in total. The possibility to attribute the unknown male plant to a cultivar was also considered and male parentage analysis was performed. Fifty-five male plants out of 63 were assigned to a definite cultivar with high confidence level. The positive result obtained in identifying males confirmed the suitability of SSR for clone fingerprinting and cultivar identification, thus opening new prospects for date palm breeding.

Transcript analysis of stress defence genes in a white poplar clone inoculated with the arbuscular mycorrhizal fungus Glomus mosseae and grown on a polluted soil.

In this study we investigated if the symbiosis with the arbuscular mycorrhizal fungus Glomus mosseae, which contributes to alleviate heavy metal stress in plants, may affect the transcription of genes involved in the stress defence in the white poplar clone 'AL35' grown on a multimetal (Cu and Zn) contaminated soil. The results obtained showed that the symbiosis with G. mosseae reduced transcript abundance of genes involved in antioxidant defence in leaves and roots of 'AL35' plants grown on the heavy metal-polluted soil. Moreover, the interaction between this poplar clone and the arbuscular mycorrhizal fungus induced the gene coding for phytochelatin synthase in leaves, whereas the expression of genes involved in heavy metal homeostasis did not change in roots. The present results suggest that, in presence of high levels of heavy metals, inoculation with G. mosseae may confer to 'AL35' a more efficient control of the oxidant level. Moreover, in mycorrhizal plants heavy metal chelation pathways appear involved in the defence strategies in leaves, whereas in roots they do not seem to contribute to increase the plant tolerance of heavy metals.

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit.

A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO(2) assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.

Molecular cloning, characterisation and expression of a manganese superoxide dismutase gene from peach (Prunus persica [L.] Batsch).

Two cDNA clones encoding mitochondrial manganese superoxide dismutases (MnSODs) from peach ( Prunus persica [L.] Batsch) were identified, which show homologies to several plant MnSODs. The amino acid sequence predicted from one full-length clone ( MnSOD1) showed the highest homology to an MnSOD from Nicotiana plumbaginifolia (94%) and included a 24-amino acid transit peptide typical of those used to target proteins to the mitochondria. A second, partial clone ( MnSOD2) showed divergence from MnSOD1 in the 3' untranslated region. It could therefore derive from a second gene or from an allele of MnSOD1. Southern hybridisation analysis suggests the existence of two MnSOD genes in peach. SOD isoenzyme profiles, MnSOD1 expression and protein levels were studied in aerial vegetative tissues derived from plants of different ages and in adult plants during the seasonal cycle. Zymograms revealed at least two isoforms of MnSODs in pre-shooting vegetative buds and in developing fruits. Levels of MnSODs were lower in leaves derived from apical shoots of adult plants than in leaves derived from seedlings, basal shoots or in vitro propagated juvenile plants, which are considered as juvenile-like structures. The MnSOD1 transcript and protein followed the same pattern. The results suggest that the steady-state levels of MnSOD1 mRNA in leaves vary with both the ontogenetic stage and the growth rate of the tissues examined.

The reduction of large molecular profiles to informative components using a genetic algorithm.

MOTIVATION: Molecular profiles (DNA fingerprints) may be used to allocate an individual of unknown membership to one among the known groups of a reference population. Time and costs of profile assessment may be reduced by identifying informative profile components (markers). RESULTS: A genetic algorithm (GA) is proposed to identify promising candidate markers from a pilot experiment in which observations are supposed to be without measurement error. The analysis of simulated datasets suggests reasonable values for GA parameters and confirms that the GA finds components of the profile showing association with the considered groups. Our GA may be used to perform a first screening of candidate markers to be included in subsequent experiments. AVAILABILITY: The 32-bit executable (Windows 95, 98 and NT) is available at http://www.ds.unifi.it/ approximately stefanin/bioinformatics.htm.

APLOGEN: an object-oriented genetic algorithm performing Monte Carlo optimization.

Problem-solving and modelling within a biological context often need a level of descriptive accuracy that is unlikely to be capable of analytical treatment, especially if the mathematical background of the biologist is poor. Furthermore solver-model maintenance is often difficult without the availability of trained specialists. Better prospects are found in the genetic algorithm field. Genetic algorithms are a set of procedures formulated to solve complex problems without specifying rules for intermediate steps. This approach becomes feasible performing a Monte Carlo simulation of the natural evolution process, in which population improvement (search for solutions) in a considered environment (the specific problem domain) is achieved by following the genetic paradigm. Starting with a randomly constituted sample of individuals, drawn from the population of admissible values and expressed as binary strings, random mating brings about individuals of the next generation. Parents are chosen with a greater probability as the number of constraints violated by each individual becomes smaller. During the constitution of each generation the presence of some genetic operators causes the improvement of population diversity and its maintenance. Genetic operators are simple string transformation rules, generally independent of a specific context. We have developed the constant core of a minimal genetic algorithm, from which can be derived genetic problem-solvers in specific domains. An applicative example--a constrained matrix equation on signed integers--is also realized to show graphically the algorithm dynamics.

An APL procedure to estimate genotype by environment interaction when two environments are considered.

Genotype by environment interaction (GEI) is a relevant topic in many fields of applied biology. Normal parametric approaches following analysis of variance are not suitable when large differences between error variances within environments are present. We illustrate an APL program following Yamada's approach to estimate GEIs and ancillary statistics when two environments are considered. The choice of APL environment is based on its value as a useful tool in algorithm implementation and problem-solving. Its use is suggested in biological applications where matrix algebra is involved and an understanding of the computing complexity of problems is generally not required.

Genetics: quantitative versus qualitative characters.

Some of the main topics regarding the inheritance of a complex trait are discussed and the relative procedure of genetic analysis described. In particular, two complementary approaches to the study of an inherited trait in humans are outlined: the biometrical approach and the proposed methodology of dissection of the complex trait into its components. Some aspects relating to the genetics of essential hypertension are used as examples.

Genetic distances based on quantitative traits.

Morphological data showing continuous distributions, polygenically controlled, may be particularly useful in intergroup classification below the species level; an appropriate distance analysis based on these traits is an important tool in evolutionary biology and in plant and animal breeding.--The interpretation of morphological distances in genetic terms is not easy because simple phenotypic data may lead to biased estimates of genetic distances. Convenient estimates can be obtained whenever it is possible to breed populations according to a suitable crossing design and to derive information from genetic parameters.--A general method for determining genetic distances is proposed. The procedure of multivariate analysis of variance is extended to estimate appropriate genetic parameters (genetic effects). Not only are optimal statistical estimates of parameters obtained but also the procedure allows the measurement of genetic distances between populations as linear functions of the estimated parameters, providing an appropriate distance matrix that can be defined in terms of these parameters. The use of the T2 statistic, defined in terms of the vector of contrasts specifying the distance, permits the testing of the significance of any distance between any pair of populations that may be of interest from a genetic point of view.--A numerical example from maize diallel data is reported in order to illustrate the procedure. In particular, heterosis effects are used as the basis for estimates of genetic divergence between populations.