Hormonal modulation of photomorphogenesis-controlled anthocyanin accumulation in tomato (Solanum lycopersicum L. cv Micro-Tom) hypocotyls: Physiological and genetic studies

Hormones are likely to be important factors modulating the light-dependent anthocyanin accumulation. Here we analyzed anthocyanin contents in hypocotyls of near isogenic Micro-Tom (MT) tomato lines carrying hormone and phytochrome mutations, as single and double-mutant combinations. In order to recapitulate mutant phenotype, exogenous hormone applications were also performed Anthocyanin accumulation was promoted by exogenous abscisic acid (ABA) and inhibited by gibberellin (GA), in accordance to the reduced anthocyanin contents measured in ABA-deficient (notabills) and GA-constitutive response (procera) mutants. Exogenous cytokinin also enhanced anthocyanin levels in MT hypocotyls. Although auxin-insensitive chageotropica mutant exhibited higher anthocyanin contents, pharmacological approaches employing exogenous auxin and a transport inhibitor did not support a direct role of the hormone in anthocyanin accumulation Analysis of mutants exhibiting increased ethylene production (epwastic) or reduced sensitivity (Never ripe), together with pharmacological data obtained from plants treated with the hormone, indicated a limited role for ethylene in anthocyanin contents. Phytochrome-deficiency (aurea) and hormone double-mutant combinations exhibited phenotypes suggesting additive or synergistic interactions, but not fully espistatic ones, in the control of anthocyanin levels in tomato hypocotyls. Our results indicate that phytochrome-mediated anthocyanin accumulation in tomato hypocotyls is modulated by distinct hormone classes via both shared and independent pathways. (C) 2010 Elsevier Ireland Ltd. All rights reserved

Spatial genetic structure of Hymenaea stigonocarpa Mart. ex Hayne assessed with chloroplast microsatellite markers

The use of chloroplast DNA markers (cpDNA) helps to elucidate questions related to ecology, evolution and genetic structure. The knowledge of inter-and intra-population genetic structure allows to design effective conservation and management strategies for tropical tree species. With the aim to help the conservation of Hymenaea stigonocarpa of the Cerrado (Brazilian savanna) in Sao Paulo State, an analysis of the spatial genetic structure (SGS) was conducted in two populations using five universal chloroplast microsatellite loci (cpSSR). The population of 68 trees of H. stigonocarpa in the Ecological Station of Itirapina (ESI) had a single haplotype, indicating a strong founder effect. In turn, the population of 47 trees of H. stigonocarpa in a contiguous area that includes the Ecological Station of Assis and the Assis State Forest (ESA), showed six haplotypes ((n) over cap (h) = 6) with a moderate haplotype diversity ((h) over cap = 0667 + 0094), revealing that it was founded by a small number of maternal lineages. The SGS analysis for the population ESA/ASF, using Moran`s I index, indicated limited seed dispersal. Considering SGS, for ex situ conservation strategies in the population ESA/ASF, seed harvesting should require a minimum distance of 750 m among seed-trees.

COMPETITION AMONG EUCALYPTUS TREES DEPENDS ON GENETIC VARIATION AND RESOURCE SUPPLY

Genetic variation and environmental heterogeneity fundamentally shape the interactions between plants of the same species. According to the resource partitioning hypothesis, competition between neighbors intensifies as their similarity increases. Such competition may change in response to increasing supplies of limiting resources. We tested the resource partitioning hypothesis in stands of genetically identical (clone-origin) and genetically diverse (seed-origin) Eucalyptus trees with different water and nutrient supplies, using individual-based tree growth models. We found that genetic variation greatly reduced competitive interactions between neighboring trees, supporting the resource partitioning hypothesis. The importance of genetic variation for Eucalyptus growth patterns depended strongly on local stand structure and focal tree size. This suggests that spatial and temporal variation in the strength of species interactions leads to reversals in the growth rank of seed-origin and clone-origin trees. This study is one of the first to experimentally test the resource partitioning hypothesis for intergenotypic vs. intragenotypic interactions in trees. We provide evidence that variation at the level of genes, and not just species, is functionally important for driving individual and community-level processes in forested ecosystems.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Genetic structure and biology of Xylella fastidiosa strains causing disease in citrus and coffee in Brazil

Xylella fastidiosa is a vector-borne, plant-pathogenic bacterium that causes disease in citrus (citrus variegated chlorosis [CVC]) and coffee (coffee leaf scorch [CLS]) plants in Brazil. CVC and CLS occur sympatrically and share leafhopper vectors; thus, determining whether X. fastidiosa isolates can be dispersed from one crop to another and cause disease is of epidemiological importance. We sought to clarify the genetic and biological relationships between CVC- and CLS-causing X. fastidiosa isolates. We used cross-inoculation bioassays and microsatellite and multilocus sequence typing (MLST) approaches to determine the host range and genetic structure of 26 CVC and 20 CLS isolates collected from different regions in Brazil. Our results show that citrus and coffee X. fastidiosa isolates are biologically distinct. Cross-inoculation tests showed that isolates causing CVC and CLS in the field were able to colonize citrus and coffee plants, respectively, but not the other host, indicating biological isolation between the strains. The microsatellite analysis separated most X. fastidiosa populations tested on the basis of the host plant from which they were isolated. However, recombination among isolates was detected and a lack of congruency among phylogenetic trees was observed for the loci used in the MLST scheme. Altogether, our study indicates that CVC and CLS are caused by two biologically distinct strains of X. fastidiosa that have diverged but are genetically homogenized by frequent recombination.

Genetic divergence is not the same as phenotypic divergence

Far too often, phenotypic divergence has been misinterpreted as genetic divergence, and based on phenotypic divergence, genetic divergence has been indicated. We have attempted to disprove this statement and call for the differentiation of phenotypic and genotypic variation.

Genetic potential of a maize population from Southern Brazil for the modified convergent-divergent selection scheme

Maize (Zea mays L.) is a very important cereal to world-wide economy which is also true for Brazil, particularly in the South region. Grain yield and plant height have been chosen as important criteria by breeders and farmers from Santa Catarina State (SC), Brazil. The objective of this work was to estimate genetic-statistic parameters associated with genetic gain for grain yield and plant height, in the first cycle of convergent-divergent half-sib selection in a maize population (MPA1) cultivated by farmers within the municipality of Anchieta (SC). Three experiments were carried out in different small farms at Anchieta using low external agronomic inputs; each experiment represented independent samples of half-sib families, which were evaluated in randomized complete blocks with three replications per location. Significant differences among half-sib families were observed for both variables in all experiments. The expected responses to truncated selection of the 25% better families in each experiment were 5.1, 5.8 and 5.2% for reducing plant height and 3.9, 5.7 and 5.0% for increasing grain yield, respectively. The magnitudes of genetic-statistic parameters estimated evidenced that the composite population MPA1 exhibits enough genetic variability to be used in cyclical process of recurrent selection. There were evidences that the genetic structure of the base population MPA1, as indicated by its genetic variability, may lead to expressive changes in the traits under selection, even under low selection pressure.

Genetic variability among sugarcane genotypes based on polymorphisms in sucrose metabolism and drought tolerance genes

Target region amplification polymorphism (TRAP) markers were used to estimate the genetic similarity (GS) among 53 sugarcane varieties and five species of the Saccharum complex. Seven fixed primers designed from candidate genes involved in sucrose metabolism and three from those involved in drought response metabolism were used in combination with three arbitrary primers. The clustering of the genotypes for sucrose metabolism and drought response were similar, but the GS based on Jaccard`s coefficient changed. The GS based on polymorphism in sucrose genes estimated in a set of 46 Brazilian varieties, all of which belong to the three Brazilian breeding programs, ranged from 0.52 to 0.9, and that based on drought data ranged from 0.44 to 0.95. The results suggest that genetic variability in the evaluated genes was lower in the sucrose metabolism genes than in the drought response metabolism ones.

Evaluation of algorithms used to order markers on genetic maps

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. Heredity (2009) 103, 494-502; doi:10.1038/hdy.2009.96; published online 29 July 2009

Genetic variability in S(1) families from different maize populations.

Genetic variability in S(1) families from different maize populations. The objectives of the present work were directed towards the study of genetic: variablilty In seven maize populations with a broad genetic base, as a guide for population improvement. The field evaluation was conducted in completely randomized blocks, at one location (Anhembi, Sao Paulo state) with different groups, of S(1) families Obtained from seven populations (GO-D: dent type, GO-F: flint type, GO-L: long car, GO-G: thick Car; and composites G3, G4 and GO-S). Estimates were obtained for genetic variance (progeny mean basis), phenotypic variance of families means, and coefficient of heritability (broad sense) for progeny means. Estimates of heritability were high for Car weight (0,89 to 0.94), car length (0.77 to 0.88) and car diameter (0.77 to 0.92); and lower for plant height (0.58 to 0.80) and Car height (0.54 to 0.84), thus showing the high Potential of the populations for recurrent selection based oil S, families. Ear yield in the base populations used as controls varied front 11,200 kg ha(-1) (GO-D) to 12,800 kg ha(-1) (G3). The means of S(1) families varied from 6,070 kg ha(-1) (GO-F) to 7,380 kg ha(-1) (G4); the Inbreeding depression in S(1) Families varied front 37.5% (G4) to 48.0% (G3) relative to the non-inbred population.

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that. has been used for estimating the average degree of dominance of quantitative trait 106 (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selling. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive X additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.

Genetic structure and mating system of Euterpe edulis Mart. populations: A comparative analysis using microsatellite and allozyme markers

A comparative study between microsatellite and allozyme markers was conducted on the genetic structure and mating system in natural populations of Euterpe edulis Mart. Three cohorts, including seedlings, saplings, and adults, were examined in 4 populations using 10 allozyme loci and 10 microsatellite loci. As expected, microsatellite markers had a much higher degree of polymorphism than allozymes, but estimates of multilocus outcrossing rate ((t) over cap (m) = 1.00), as well as estimates of genetic structure (F(IS), G(ST)), were similar for the 2 sets of markers. Estimates of R(ST), for microsatellites, were higher than those of GST, but results of both statistics revealed a close agreement for the genetic structure of the species. This study provides support for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters. Effects of sample size on estimates from hypervariable loci are also discussed in this paper.

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA x CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.

Genetic Diversity and a PCR-Based Method for Xanthomonas axonopodis Detection in Passion Fruit

Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the purple and yellow passion fruit as well as the sweet passion fruit. The diversity of 87 isolates of pv. passiflorae collected from across 22 fruit orchards in Brazil was evaluated using molecular profiles and statistical procedures, including an unweighted pair-group method with arithmetical averages-based dendrogram, analysis of molecular variance (AMOVA), and an assigning test that provides information on genetic structure at the population level. Isolates from another eight pathovars were included in the molecular analyses and all were shown to have a distinct repetitive sequence-based polymerase chain reaction profile. Amplified fragment length polymorphism technique revealed considerable diversity among isolates of pv. passiflorae, and AMOVA showed that most of the variance (49.4%) was due to differences between localities. Cluster analysis revealed that most genotypic clusters were homogeneous and that variance was associated primarily with geographic origin. The disease adversely affects fruit production and may kill infected plants. A method for rapid diagnosis of the pathogen, even before the disease symptoms become evident, has value for producers. Here, a set of primers (Xapas) was designed by exploiting a single-nucleotide polymorphism between the sequences of the intergenic 16S-23S rRNA spacer region of the pathovars. Xapas was shown to effectively detect all pv. passiflorae isolates and is recommended for disease diagnosis in passion fruit orchards.

Genetic transformation of Citrus sinensis cv. Hamlin with hrpN gene from Erwinia amylovora and evaluation of the transgenic lines for resistance to citrus canker

Transgenic Citrus sinensis (L.) Osb. cv. Hamlin plants expressing the hrpN gene were obtained by Agrobacterium tumefaciens (Smith and Towns) Conn-mediated transformation. hrpN encodes a harpin protein, which elicits the hypersensitive response and systemic acquired resistance in plants. The gene construct consisted of gst1, a pathogen-inducible promoter, a signal peptide for protein secretion to the apoplast, the selection genes nptI1 or aacC1 and the Nos terminator. The function of gst1 in citrus was evaluated in transgenic C. sinensis cv. Valencia harboring the reporter gene uidA (gus) driven by this promoter. Histochemical analysis for gus revealed that gst1 is activated in citrus leaves by both wounding and inoculation with Xanthomonas axonopodis Starr and Garces pv. citri (Hasse) Vauterin et al. Genetic transformation was confirmed by Southern blot hybridization in eight cv. Hamlin acclimatized plants. RT-PCR confirmed hrpN gene expression in seven cv. Hamlin transgenic lines before pathogen inoculation. Some hrpN transgenic lines showed severe leaf curling and abnormal growth. Six hrpN transgenic lines were propagated and evaluated for susceptibility to X axonopodis pv. citri. RT-PCR confirmed gene expression in all six hrpN transgenic lines after pathogen inoculation. Several of the hrpN transgenic lines showed reduction in susceptibility to citrus canker as compared with non-transgenic plants. One hrpN transgenic line exhibited normal vegetative development and displayed very high resistance to the pathogen, estimated as up to 79% reduction in disease severity. This is the first report of genetic transformation of citrus using a pathogen-inducible promoter and the hrpN gene. Further evaluations of the transgenic plants under field conditions are planned. Nevertheless, the evidence to date suggests that the hrpN gene reduces the susceptibility of citrus plants to the canker disease. (C) 2009 Elsevier B.V. All rights reserved.