Real-time quantitative PCR assays for evaluation of soybean varieties for resistance to the stem and root rot pathogen Phytophthora sojae

Phytophthora root and stem rot caused by Phytophthora sojae is one of the most destructive disease of soybeans in the world. Effective management of the disease depends on selection and use of soybean varieties resistant to the disease. Fast and reliable procedures are vital to screen soybean varieties against the pathogen. Novel real-time quantitative (qPCR) assays were developed for both absolute and relative quantification of P. sojae in infected root tissues. QPCR assays were based on the detection of the internal transcribed spacer (ITS) gene of the pathogen and 18S ribosomal gene of the host plant. Absolute qPCR allowed the detection of as low as 10 femtograms (fg) of P. sojae DNA in soybean roots. Relative qPCR, employing the comparative threshold cycle (Ct) method, was effective and reliable for quantification of P. sojae DNA normalized to plant DNA in infected soybean root tissues. P. sojae DNA quantities detected in both qPCR assays had high correlations with disease severity index (DSI) ratings of soybean varieties. QPCR assays developed in this study were useful for determination of the levels of P. sojae DNA in different varieties of soybean and for evaluation of them for relative resistance to the pathogen.     

How long should we measure? An exploration of factors controlling the inter-annual variation of catchment sediment yield

Purpose  

Although it is well-known that catchment suspended sediment yields (SY; tons per square kilometre per year) can vary significantly from year to year, little information exists on the magnitude and factors controlling this variability. This is crucial to assess the reliability of average SY values for a given measuring period (MP) and is of great geomorphic significance. This paper aims to bridge this research gap.     

The financial feasibility of small‐scale grouper aquaculture in the Philippines

Abstract

This paper presents the results of an economic analysis of the aquaculture of two species of grouper E. coloides (orange‐spotted grouper, green grouper, red‐spotted grouper) and E. malabaricus (malabar grouper, black‐spotted grouper) for small producers in the Philippines. The findings of the analysis indicate that, based on the assumptions, grouper culture is financially feasible. However, the capital requirements for the broodstock, hatchery/nursery, and integrated system may be beyond the financial means of many small producers. These stages of grouper culture may need to be developed as a larger project by private investors or government. The capital investment requirement for grow‐out (not including purchase of transport boxes) is within the financial means of small producers. Loans or other incentives will need to be made available for the small producer, but the cash flow indicates that these loans can be repaid in the first year of production.     

Oviposition and Larval Habitat Preferences of the Saltwater Mosquito, Aedes vigilax, in a Subtropical Mangrove Forest in Queensland, Australia

Abstract Our aim was to investigate the oviposition and larval habitats of the saltwater mosquito Aedes vigilax (Skuse) (Diptera: Culicidae) in a mangrove forest system in subtropical Queensland, Australia. Eggshells (indicators of oviposition) and larvae were sampled in three habitat classes that were depicted in a schematic model. Two classes were in depressions or basins, either with hummocks or dense pneumatophore substrates, both of which retained water after tidal flooding. The third class was in freely flushed mangroves that corresponded with more frequent tidal connections than the depression classes. ANOVA and Tukey-Kramer tests were used to analyze the data. The null hypotheses were rejected: the hummock class was a significant habitat based on both eggshell and larval data. The conclusion was that mosquito production in the mangrove system was distributed unevenly between habitat classes, and that the hummock class had conditions suited to the requirements of the immature stages of Ae. vigilax. This research has the potential to inform mosquito management strategies by focusing treatment on the problem habitats and underpinning habitat modifications including reducing water retention in the basins.     

Methods of analysis for georeferenced sample counts of tarnished plant bugs in cotton

The problem of analyzing georeferenced cotton pest insect samples when a large percentage of the counts are zero is examined. The use of appropriate statistical methods for their analysis is required. To demonstrate this, georeferenced samples (n = 63) of tarnished plant bugs (TPBs; Lygus lineolaris [Palisot de Beauvois] (Heteroptera: Miridae)) were analyzed by three statistical methods and the results were compared. Correlation analysis of the sample counts with 25 classes of cotton growth derived from an unsupervized classification of multispectral imagery was followed by a complete enumeration analysis comprising three scenarios. The first scenario assumed the insect samples were unstratified. A distribution of sample averages was created by complete enumeration of all combinations of samples taken four at a time. The second scenario used imagery of the cotton fields to allocate the samples among three cotton growth categories (marginal, good or best) derived by a supervized classification of the 25 unsupervized classes. The insect samples associated with these categorical habitats were completely enumerated using allocations of 4, 6, 8 or 10 samples at a time from various sample sizes to determine how different allocations affected the results. The mean was not affected, but the standard deviation decreased with increased allocation sizes in all habitats. The third scenario used the two observers and three habitat categories to create six additional complete enumeration distributions by allocating four samples at a time from groups of varying sample sizes. These enumeration distributions are non-parametric estimators of the sampling distribution of: (1) the sample averages of a given sample size when samples are taken from the entire field, (2) the sample averages of a given size when samples are taken from each cotton habitat or (3) the sample averages of a given sample size from samples taken from each habitat by each observer. To support the enumeration analyses, these insect samples were analyzed further by Poisson regression models. These models showed significant differences between TPB counts by the two observers and among the habitats, whereas the observer by habitat interaction was not significant. For every combination of observer and cotton growth category, a Poisson regression model estimated the mean rate of TPB numbers. These means were similar to the corresponding modes of the complete enumeration distributions. The two non-standard methods showed that TPB numbers differed by habitat categories even though there were samples with a zero count, whereas a correlation analysis failed to identify a relationship between TPB sample counts and unsupervized habitat classes.     

Biofloc technology in intensive broodstock farming of the pink shrimp Farfantepenaeus duorarum: spawning performance,biochemical composition and fatty acid profile of eggs

A 45‐day trial was performed to evaluate the effect of biofloc technology (BFT) with or without fresh food (FF) supplementation during pre‐maturation period on Farfantepenaeus duorarum spawning performance, biochemical composition and fatty acid profile of eggs as compared with conventional clear‐water system (CW+FF). Females raised in biofloc and that received FF supplementation (FLOC+FF) achieved better spawning performance in terms of number of eggs per spawn (49 × 10³), number of eggs per spawn per g of spawner's body weight (2.1 × 10³) and egg size (~275 μm) as compared with CW+FF (23 × 10³, 1.1 × 10³ and 263 μm respectively), but both treatments did not vary from FLOC (P > 0.05). High spawning activity was also observed in biofloc system as compared with clear‐water system as shown in number of spawns per ablated female (2.2–3.0 versus 0.6) and percentage of females that spawn at least once (80–82 versus 25%). Biochemical composition of eggs presented no significant differences among treatments. FA profile of eggs indicated that high spawning activity performed by females in FLOC+FF treatment was reflected in lower mean levels of EPA, DHA and sum of polyunsaturated fatty acids (n‐3) and (n‐6). The better reproductive performance demonstrated by females raised in biofloc justified the application of this technology in F. duorarum broodstock.     

Bilateral renal agenesis in an alpaca cria

A 3-day-old male alpaca cria was presented for lack of vigor and failure to urinate since birth. Based on the history, laboratory data, ultrasonographs, surgical findings, and postmortem examination, the cria was diagnosed with bilateral renal agenesis and hypoplastic bladder, a congenital condition rarely seen in veterinary medicine.     

Determination of free amino compounds in betalainic fruits and vegetables by gas chromatography with flame ionization and mass spectrometric detection

Amino acids and amines are the precursors of betalains. Therefore, the profiles of free amino compounds in juices obtained from cactus pears [Opuntia ficus-indica (L.) Mill. cv. Bianca, cv. Gialla, and cv. Rossa], pitaya fruits [Selenicereus megalanthus (K. Schumann ex Vaupel) Moran, Hylocereus polyrhizus (Weber) Britton & Rose, and Hylocereus undatus (Haworth) Britton & Rose], and in extracts from differently colored Swiss chard [Beta vulgaris L. ssp. cicla (L.) Alef. cv. Bright Lights] petioles and red and yellow beets (B. vulgaris L. ssp. vulgaris var. conditiva Alef. cv. Burpee's Golden) were investigated for the first time. Amino compounds were derivatized with propyl chloroformate. While gas chromatography (GC) with mass spectrometry was used for peak assignment, GC flame ionization detection was applied for quantification of individual compounds. Whereas proline was the major free amino compound of cactus pear and pitaya fruit juices, glutamine dominated in Swiss chard stems and beets, respectively. Interestingly, extremely high concentrations of dopamine were detected in Swiss chard stems and beets. Furthermore, the cleavage of betaxanthins caused by derivatization in alkaline reaction solutions is demonstrated for the first time. Amino acids and amines thus released might increase the actual free amino compound contents of the respective sample. To evaluate the contribution of betaxanthin cleavage to total amino acid and amine concentration, isolated betaxanthins were derivatized according to the "EZ:faast" method prior to quantification of the respective amino compounds released. On a molar basis, betaxanthin contribution to overall amino compound contents was always below 6.4%.     

Trace metal concentrations in Posidonia oceanica of North Corsica (northwestern Mediterranean Sea): use as a biological monitor?

Background  

Within semi-closed areas like the Mediterranean Sea, anthropic wastes tend to concentrate in the environment. Metals, in particular, are known to persist in the environment and can affect human health due to accumulation in the food chain. The seagrass Posidonia oceanica, widely found in Mediterranean coastal waters, has been chosen as a "sentinel" to quantify the distribution of such pollutants within the marine environment. Using a technique similar to dendrochronology in trees, it can act as an indicator of pollutant levels over a timeframe of several months to years. In the present study, we measured and compared the levels of eight trace metals (Cr, Ni, Cu, Zn, As, Se, Cd, and Pb) in sheaths dated by lepidochronology and in leaves of shoots sampled from P. oceanica meadows collected from six offshore sites in northern Corsica between 1988 and 2004; in the aim to determine 1) the spatial and 2) temporal variations of these metals in these areas and 3) to compared these two types of tissues.     

Genetic architecture of adult plant resistance to leaf rust in a wheat association mapping panel

Leaf rust caused by Puccina triticina is one of the most destructive fungal diseases of wheat (Triticum aestivum). Adult plant resistance (APR) is an effective strategy to achieve long‐term protection from the disease. In this study, findings are reported from a genome‐wide association study (GWAS) using a panel of 96 wheat cultivars genotyped with 874 Diversity Arrays Technology (DArT) markers and tested for adult leaf rust response in six field trials. A total of 13 quantitative trait loci (QTL) conferring APR to leaf rust were identified on chromosome arms 1BL, 1DS, 2AS, 2BL, 2DS, 3BS, 3BL, 4AL, 6BS (two), 7DS, 5BL/7BS and 6AL/6BS. Of these, seven QTLs mapped close to known resistance genes and QTLs, while the remaining six are novel and can be used as additional sources of resistance. Accessions with a greater number of combined QTLs for APR showed lower levels of disease severity, demonstrating additive and significant pyramiding effects. All QTLs had stable main effects and they did not exhibit a significant interaction with the experiments. These findings could help to achieve adequate levels of durable resistance through marker‐assisted selection and pyramiding resistance QTLs in local germplasm.