Identification of microsatellites markers associated with yield components and quality parameters in sugarcane

Marker assisted selection depends on the identification of tightly linked association between marker and the trait of interest. In the present work, functional (EST-SSRs) and genomic (gSSRs) microsatellite markers were used to detect putative QTLs for sugarcane yield components (stalk number, diameter and height) and as well as for quality parameters (Brix, Pol and fibre) in plant cane. The mapping population (200 individuals) was derived from a bi-parental cross (IACSP95-3018 x IACSP93-3046) from the IAC Sugarcane Breeding Program. As the map is under construction, single marker trait association analysis based on the likelihood ratio test was undertaken to detect the QTLs. Of the 215 single dose markers evaluated (1:1 and 3:1), 90 (42%) were associated with putative QTLs involving 43 microsatellite primers (18 gSSRs and 25 EST-SSRs). For the yield components, 41 marker/trait associations were found: 20 for height, 6 for diameter and 15 for stalk number. An EST-SSRs marker with homology to non-phototropic hypocotyls 4 (NPH4) protein was associated with a putative QTL with positive effect for diameter as also with a negative effect for stalk number. In relation to the quality parameters, 18 marker trait associations were found for Brix, 19 for Pol, and 12 for fibre. For fibre, 58% of the QTLs detected showed a negative effect on this trait. Some makers associated with QTLs with a negative effect for fibre showed a positive effect for Pol, reflecting the negative correlation generally observed between these traits.

Diversity of endophytic yeasts from sweet orange and their localization by scanning electron microscopy

Endophytes are microorganisms that colonize plant tissues internally without causing harm to the host. Despite the increasing number of studies on sweet orange pathogens and endophytes, yeast has not been described as a sweet orange endophyte. In the present study, endophytic yeasts were isolated from sweet orange plants and identified by sequencing of internal transcribed spacer (ITS) rRNA. Plants sampled from four different sites in the state of Sao Paulo, Brazil exhibited different levels of CVC (citrus variegated chlorosis) development. Three citrus endophytic yeasts (CEYs), chosen as representative examples of the isolates observed, were identified as Rhodotorula mucilaginosa, Pichia guilliermondii and Cryptococcus flavescens. These strains were inoculated into axenic Citrus sinensis seedlings. After 45 days, endophytes were reisolated in populations ranging from 10(6) to 10(9) CFU/g of plant tissue, but, in spite of the high concentrations of yeast cells, no disease symptoms were observed. Colonized plant material was examined by scanning electron microscopy (SEM), and yeast cells were found mainly in the stomata and xylem of plants, reinforcing their endophytic nature. P. guilliermondii was isolated primarily from plants colonized by the causal agent of CVC, Xylella fastidiosa. The supernatant from a culture of P. guilliermondii increased the in vitro growth of X. fastidiosa, suggesting that the yeast could assist in the establishment of this pathogen in its host plant and, therefore, contribute to the development of disease symptoms.

Evaluation of citrus somatic hybrids for tolerance to Phytophthora nicotianae and citrus tristeza virus

Somatic hybridization is a biotechnology tool that can be used in citrus breeding programs to produce somatic hybrids with the complete genetic combination of both parents. The goal of this work was to test the reaction of citrus somatic hybrids that may be useful as rootstocks to trunk and root infections caused by Phytophthora nicotianae van Breda de Haan (P parasitica Dastur) and to citrus tristeza virus (CTV). The somatic hybrids evaluated were `Caipira` sweet orange (Citrus sinensis L. Osbeck) + `Rangpur` lime (C. limonia Osbeck), `Caipira` sweet orange + `Cleopatra` mandarin (C. reshni hort. ex Tanaka), `Caipira` sweet orange + `Volkamer` lemon (C. volkameriana V Ten. & Pasq.), `Caipira` sweet orange + rough lemon (C. jambhiri Lush.), `Cleopatra` mandarin + `Volkamer` lemon, `Cleopatra` mandarin + sour orange (C. aurantium L.), `Rangpur` lime + `Sunki` mandarin (C. sunki (Hayata) hort. ex Tanaka), `Ruby Blood` sweet orange (C. sinensis L. Osbeck) + `Volkamer` lemon, `Rohde Red` sweet orange (C. sinensis L. Osbeck) + `Volkamer` lemon, and `Valencia` sweet orange + Fortunella obovata hort. ex Tanaka. For P. nicotianae trunk and root infection assays, plants of the somatic hybrids, obtained from 9-month semi-hardwood cuttings, were evaluated and compared with diploid citrus rootstock cultivars after mycelia inoculation in the trunk or spore infestation in the substrate, respectively. `Cleopatra` mandarin + sour orange, `Rangpur` lime + `Sunki` mandarin, `Cleopatra` mandarin + `Volkamer` lemon, `Ruby Blood` sweet orange + `Volkamer` lemon, `Rohde Red` sweet orange + `Volkamer` lemon, and `Caipira` sweet orange + `Volkamer` lemon had less trunk rot occurrence, whereas the somatic hybrids `Cleopatra` mandarin + `Volkamer` lemon, `Cleopatra` mandarin + sour orange, `Caipira` sweet orange + `Volkamer` lemon, and `Caipira` sweet orange + `Rangpur` lime were tolerant to root rot. For CTV assays, plants of the somatic hybrids along with tolerant and intolerant rootstocks were budded with a mild strain CTV-infected or healthy `Valencia` sweet orange budwood. Differences in average scion shoot length indicated that the hybrids `Cleopatra` mandarin + sour orange and `Valencia` sweet orange + Fortunella obovata were intolerant to CTV (c) 2007 Elsevier B.V. All rights reserved.

Parameterization and Evaluation of Predictions of DSSAT/CANEGRO for Brazilian Sugarcane

The DSSAT/CANEGRO model was parameterized and its predictions evaluated using data from five sugarcane (Sacchetrum spp.) experiments conducted in southern Brazil. The data used are from two of the most important Brazilian cultivars. Some parameters whose values were either directly measured or considered to be well known were not adjusted. Ten of the 20 parameters were optimized using a Generalized Likelihood Uncertainty Estimation (GLUE) algorithm using the leave-one-out cross-validation technique. Model predictions were evaluated using measured data of leaf area index (LA!), stalk and aerial dry mass, sucrose content, and soil water content, using bias, root mean squared error (RMSE), modeling efficiency (Eff), correlation coefficient, and agreement index. The Decision Support System for Agrotechnology Transfer (DSSAT)/CANEGRO model simulated the sugarcane crop in southern Brazil well, using the parameterization reported here. The soil water content predictions were better for rainfed (mean RMSE = 0.122mm) than for irrigated treatment (mean RMSE = 0.214mm). Predictions were best for aerial dry mass (Eff = 0.850), followed by stalk dry mass (Eff = 0.765) and then sucrose mass (Eff = 0.170). Number of green leaves showed the worst fit (Eff = -2.300). The cross-validation technique permits using multiple datasets that would have limited use if used independently because of the heterogeneity of measures and measurement strategies.

Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria

Pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite produced by a narrow range of Gram-negative bacteria. The PRN biosynthesis by rhizobacteria presumably has a key role in their life strategies and in the biocontrol of plant diseases. The biosynthetic operon that encodes the pathway that converts tryptophan to PRN is composed of four genes, prnA through D, whose diversity, genomic context and spread over bacterial genomes are poorly understood. Therefore, we launched an endeavour aimed at retrieving, by in vitro and in silico means, diverse bacteria carrying the prnABCD biosynthetic loci in their genomes. Analysis of polymorphisms of the prnD gene sequences revealed a high level of conservation between Burkholderia, Pseudomonas and Serratia spp. derived sequences. Whole-operon- and prnD-based phylogeny resulted in tree topologies that are incongruent with the taxonomic status of the evaluated strains as predicted by 16S rRNA gene phylogeny. The genomic composition of c. 20 kb DNA fragments containg the PRN operon varied in different strains. Highly conserved and distinct transposase-encoding genes surrounding the PRN biosynthetic operons of Burkholderia pseudomallei strains were found. A prnABCD-deprived genomic region in B. pseudomallei strain K96243 contained the same gene composition as, and shared high homology with, the flanking regions of the PRN operon in B. pseudomallei strains 668, 1106a and 1710b. Our results strongly suggest that the PRN biosynthetic operon is mobile. The extent, frequency and promiscuity of this mobility remain to be understood.

Overwintering of Sclerotium rolfsii and S-rolfsii var. delphinii in different latitudes of the United States

Previously known only from the southern United States, hosta petiole rot recently appeared in the northern United States. Sclerotium rolfsii var. delphinii is believed to be the predominant petiole rot pathogen in the northern United States, whereas S. rolfsii is most prevalent in the southern United States. In order to test the hypothesis that different tolerance to climate extremes affects the geographic distribution of these fungi, the survival of S. rolfsii and S. rolfsii var. delphinii in the northern and southeastern United States was investigated. At each of four locations, nylon screen bags containing sclerotia were placed on the surface of bare soil and at 20-cm depth. Sclerotia were recovered six times from November 2005 to July 2006 in North Dakota and Iowa, and from December 2005 to August 2006 in North Carolina and Georgia. Survival was estimated by quantifying percentage of sclerotium survival on carrot agar. Sclerotia of S. rolfsii var. delphinii survived until at least late July in all four states. In contrast, no S. rolfsii sclerotia survived until June in North Dakota or Iowa, whereas 18.5% survived until August in North Carolina and 10.3% survived in Georgia. The results suggest that inability to tolerate low temperature extremes limits the northern range of S. rolfsii.

Stone fruit injuries and damage at the wholesale market of Sao Paulo, Brazil

Mechanical injuries and diseases in stone fruit are important causes for market rejection. The objectives of this research were to quantify and characterize the mechanical injuries and diseases in peaches, nectarines and plums at Sao Paulo`s wholesale market, the largest in Brazil. Incidence of injuries was assessed weekly in 1 % of the marketed fruit (2973 fruit/week), from September to December in 2003 and 2004. Mechanical injuries were the most frequent injuries in both years, ranging from 8.73% (plum) to 44.5% (nectarine) of injured fruit. There was a significant positive correlation between the incidence of postharvest mechanical injuries and postharvest diseases. Incidence of postharvest diseases varied from 2.5% to 6.6%. Cladosporium rot (Cladosporium sp.) and brown rot (Monilinia fructicola) were the most frequent diseases, and were mostly detected in the apexes of nectarines and peaches. Aurora (peach), Sunraycer (nectarine) and Gulfblaze (plum) varieties were the most susceptible to injuries and diseases. (c) 2007 Elsevier B.V. All rights reserved.

The proportion of individual lucerne plants resistant to Phytophthora medicaginis and Colletotrichum trifolii in Australian cultivars

Phytophthora root rot (Phytophthora medicaginis) and colletotrichum crown rot (Colletotrichum trifoli) are the 2 most serious pathogens of lucerne in eastern Australia. Work reported in this paper shows that in glasshouse tests of the 11 most commonly grown Australian lucerne cultivars, the proportion of individual plants with resistance to both pathogens ranges from 0 (Hunter River and Aurora) through to a maximum of 19.8% (Sequel HR). Within 9 of the cultivars, the proportion of individual plants resistant to the 2 pathogens was <7%. Since these 2 diseases are known to cause serious losses in eastern Australia, the results indicate further improvement in lucerne production can be obtained by increasing the proportion of individual plants in a cultivar resistant to both pathogens. This would be best achieved by identifying dominant sources of resistance and incorporating this into on-going lucerne breeding programs.

A sponge/dinoflagellate association in the haplosclerid sponge Haliclona sp.: cellular origin of cytotoxic alkaloids by Percoll density gradient fractionation

Light-microscopic and electron-microscopic studies of the tropical marine sponge Haliclona sp. (Or der: Haplosclerida Family: Haliclonidae) from Heron Island, Great Barrier Reef, have revealed that this sponge is characterized by the presence of dinoflagellates and by nematocysts. The dinoflagellates are 7-10 mu m in size, intracellular, and contain a pyrenoid with a single stalk, whereas the single chloroplast is branched, curved, and lacks grana. Mitochondria are present, and the nucleus is oval and has distinct chromosomal structure. The dinoflagellates are morphologically similar to Symbiodinium microadriaticum, the common intracellular symbiont of corals, although more detailed biochemical and molecular studies are required to provide a precise taxonomic assignment. The major sponge cell types found in Haliclona sp, are spongocytes, choanocytes, and archaeocytes; groups of dinoflagellates are enclosed within large vacuoles in the archaeocytes. The occurrence of dinoflagellates in marine sponges has previously been thought to be restricted to a small group of sponges including the excavating hadromerid sponges; the dinoflagellates in these sponges are usually referred to as symbionts. The role of the dinoflagellates present in Haliclona sp. as a genuine symbiotic partner requires experimental investigation. The sponge grows on coral substrates, from which it may acquire the nematocysts, and shows features, such as mucus production, which are typical of some excavating sponges. The cytotoxic alkaloids, haliclonacyclamines A and B, associated with Haliclona sp. are shown by Percoll density gradient fractionation to be localized within the sponge cells rather than the dinoflagellates. The ability to synthesize bioactive compounds such as the haliclonacyclamines may help Haliclona sp. to preserve its remarkable ecological niche.

Changes in the racial composition of Phytophthora sojae in Australia between 1979 and 1996

Surveys of commercial soybean fields, disease nurseries, and trial plots of soybean were conducted throughout eastern Australia between 1979 and 1996, and 694 isolates of Phytophthora sojae were collected and classified into races. Fourteen races, 1, 2, 4, 10, 15, and 25, and eight new races, 46 to 53, were identified, but only races 1, 4, 15, 25, 46, and 53 were found in commercial fields. Races 1 and 15 were the only races found in commercial fields in the soybean-growing areas of Australia up until 1989, with race 1 being the dominant race. Race 4 was found in central New South Wales in 1989 on cultivars with the Rps1a gene, and it is now the dominant race in central and southern New South Wales. Races 46 and 53 have only been found once, in southern New South Wales, and race 25 was identified in the same region in 1994 on a cultivar with the Rps1k gene. Only races 1 and 15 have been found in the northern soybean-growing regions, with the latter dominating, which coincides with the widespread use of cultivars with the Rps2 gene. Changes in the race structure of the P. sojae population from commercial fields in Australia follow the deployment of specific resistance genes.

Gene and genotypic diversity of Phytophthora cinnamomi in South Africa and Australia revealed by DNA polymorphisms

Phytophthora cinnamomi isolates from South Africa and Australia were compared to assess genetic differentiation between the two populations. These two populations were analysed for levels of phenotypic diversity using random amplified polymorphic DNAs (RAPDs) and gene and genotypic diversity using restriction fragment length polymorphisms (RFLPs). Sixteen RAPD markers from four decanucleotide Operon primers and 34 RFLP alleles from 15 putative loci were used. A few isolates from Papua New Guinea known to posses alleles different from Australian isolates were also included for comparative purposes. South African and Australian P. cinnamomi populations were almost identical with an extremely low level of genetic distance between them (D-m = 0.003). Common features for the two populations include shared alleles, low levels of phenotypic/genotypic diversity, high clonality, and low observed and expected levels of heterozygosity. Furthermore, relatively high levels of genetic differentiation between mating type populations (D-m South Africa = 0.020 and D-m Australia = 0.025 respectively), negative fixation indices, and significant deviations from Hardy-Weinberg equilibrium, all provided evidence for the lack of frequent sexual reproduction in both populations. The data strongly suggest that both the South African and Australian P. cinnamomi populations are introduced.

Spermatophore and Gonopore Morphology of the Southwestern-Atlantic Hermit Crab Pagurus exilis (Benedict, 1892) (Anomura, Paguridae)

Marcelo A. Scelzo, Marina Z. Fantucci, and Fernando L. Mantelatto (2010) Spermatophore and gonopore morphology of the southwestern-Atlantic hermit crab Pagurus exilis (Benedict, 1892) (Anomura, Paguridae). Zoological Studies 49(3): 421-433. The form and function of the spermatophore have been used as a complementary tool in studies of the reproductive biology and systematics of hermit crabs. In this context, we describe the spermatophore and gonopore morphology of Pagurus exilis. The spermatophores were extracted from the distal part of the vas deferens of specimens collected in Argentina and Brazil. The spermatophores were composed of 3 major regions: a main ampulla (with a sperm capsule inside and an accessory ampulla at the base), a stalk, and a pedestal. Each spermatophore had a distinct dorsolateral suture line around the ampulla, where the rupture occurs to release the sperm. The spermatophore total length was 1.5 times the main ampulla length. The main ampulla was oval and slightly flattened. A triangular accessory ampulla extended from the main ampulla base to the pedestal on 1 side, and contained no to several sperm. The stalk is short and flattened, and as wide as the main ampulla. One to 3 spermatophores were found attached to each pedestal, which was almost oblong in shape. The dimensions of the spermatophore and its component parts were directly influenced by the size of the hermit crab. Gonopores of males were covered by long pappose setae, while female gonopores bore a few short cuspidate setae. Specimens from Brazil and Argentina had the same spermatophore morphology, corroborating the previously observed absence of genetic differences between the both populations. The spermatophore morphology of this species has similarities with the broad general pattern of the Paguridae, being most similar to one of the (at least) 3 patterns of spermatophore morphology described for Pa gurus. http://zoolstud.sinica.edu.tw/Journals/49.3/421.pdf

Morphological and morphometric appraisal of the spermatophore of the southern hermit crab Isocheles sawayai Forest and Saint Laurent, 1968 (Anomura: Diogenidae), with comments on gonopores in both sexes

The spermatophore morphology of the hermit crab Isocheles sawayai from Southwestern Atlantic (Brazil) is described. The spermatophores show similarities with those described for other members of the family Diogenidae, especially with the recently described Loxopagurus loxochelis. The spermatophore is composed of three major regions: a sperm filled head or ampulla, a columnar stalk and a foot or pedestal. The spermatophores show specific morphology in having a circular ampulla, and a constriction or neck between the ampulla (100 mu m) and the thin (27 mu m), long stalk (500 mu m). The stalk penetrates less than half way into the spermatophore head. Most spermatophores show one or the small posterior projections on the underside of the ampulla as being bigger than the other, making it asymmetrical. The size of the spermatophore is related to hermit crab size with direct relationships found between spermatophore ampulla width, total length, and peduncle length with shield length of the hermit crab. The morphological characteristics of the spermatophore of L sawayai. are species-specific distinguishing it from other members of the family, and are useful to infer further phylogenetic relationships. (C) 2008 Elsevier GmbH. All rights reserved.

Expression of resistance by tetraploid and diploid lucerne genotypes to Phytophthora medicaginis is not influenced by inoculum level or by temperature

Phytophthora-resistant lucerne cultivars do not always perform well under conditions of high disease pressure in the field. To determine whether resistance expression remains stable under different infection intensities, tetraploid and diploid lucerne genotypes, genotypically defined for their reactions to Phytophthora medicaginis, were clonally propagated, and the influence of different reproducible inoculum levels (0 . 5 and 5 . 0 g dry weight mycelium/kg dry weight potting mix), the period of exposure to these levels (10-60 days), and temperature (16/22 degrees C and 24/30 degrees C) on disease expression was determined in controlled environments. Generally, expression of resistance by resistant genotypes, remained stable under these conditions. Biotic (e.g. Aphanomyces eutiches) or abiotic factors other than P. medicaginis may be responsible for the poorer than expected performance under field conditions in some instances, or the percentage of resistant plants in some cultivars currently classified as resistant is insufficient to provide buffering against productivity reductions under severe epidemics. Further research is needed to clarify the situation.

Differential disease reactions on lucerne genotypes inoculated with Phytophthora medicaginis isolates from lucerne and chickpea

Stem inoculation of clonally propagated lucerne genotypes was used to assess levels of host species and genotype specialisation in Phytophthora medicaginis. A quantitative assessment of pathogenic aggressiveness of 29 P. medicaginis isolates (from lucerne and chickpea) on 9 different clonally propagated lucerne genotypes revealed no significant difference in aggressiveness between isolates from lucerne and those from chickpea on all of the lucerne genotypes. This supported previous studies which showed that P. medicaginis isolates from lucerne and chickpea were indistinguishable using random amplified polymorphic DNA (RAPD) analysis. Analysis of pathogenic aggressiveness towards individual lucerne genotypes revealed, for the first time, specificity of individual P. medicaginis isolates. This has implications for breeding for resistance to P. medicaginis in lucerne, where screening should be done using the widest range of pathogen specificity obtainable.