A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective. (C) 2012 The Authors Journal of Fish Biology (C) 2012 The Fisheries Society of the British Isles

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense

Fusarium oxysporum f. sp. cubense (Foc), causal agent of fusarium wilt of banana, is among the most destructive pathogens of banana and plantain. The development of a molecular diagnostic capable of reliably distinguishing between the various races of the pathogen is of key importance to disease management. However, attempts to distinguish isolates using the standard molecular loci typically used for fungal phylogenetics have been complicated by a poor correlation between phylogeny and pathogenicity. Among the available alternative loci are several putative effector genes, known as SIX genes, which have been successfully used to differentiate the three races of F. oxysporum f. sp. lycopersici. In this study, an international collection of Foc isolates was screened for the presence of the putative effector SIX8. Using a PCR and sequencing approach, variation in Foc-SIX8 was identified which allowed race 4 to be differentiated from race 1 and 2 isolates, and tropical and subtropical race 4 isolates to be distinguished from one another.

Molecular phylogenetic analysis reveals six new species of Diaporthe from Australia

Six new species of Diaporthe, D. beilharziae on Indigofera australis, D. fraxini-angustifoliae on Fraxinus angustifolia subsp. oxycarpa, D. litchicola on Litchi chinensis, D. nothofagi on Nothofagus cunninghamii, D. pascoei on Persea americana and D. salicicola on Salix purpurea from Australia are described and illustrated based on morphological characteristics and molecular analyses. Three of the new species no longer produced sporulating structures in culture and two of these were morphologically described from voucher specimens. Phylogenetic relationships of the new species with other Diaporthe species are revealed by DNA sequence analyses based on the internal transcribed spacer (ITS) region, and partial regions of the β-tubulin (BT) and translation elongation factor 1-alpha (TEF). © 2013 Mushroom Research Foundation.

Wheat biomass and yield increased when populations of the root-lesion nematode (Pratylenchus thornei) were reduced through sequential rotation of partially resistant winter and summer crops

The root-lesion nematode, Pratylenchus thornei, can reduce wheat yields by >50%. Although this nematode has a broad host range, crop rotation can be an effective tool for its management if the host status of crops and cultivars is known. The summer crops grown in the northern grain region of Australia are poorly characterised for their resistance to P. thornei and their role in crop sequencing to improve wheat yields. In a 4-year field experiment, we prepared plots with high or low populations of P. thornei by growing susceptible wheat or partially resistant canaryseed (Phalaris canariensis); after an 11-month, weed-free fallow, several cultivars of eight summer crops were grown. Following another 15-month, weed-free fallow, P. thornei-intolerant wheat cv. Strzelecki was grown. Populations of P. thornei were determined to 150 cm soil depth throughout the experiment. When two partially resistant crops were grown in succession, e.g. canaryseed followed by panicum (Setaria italica), P. thornei populations were <739/kg soil and subsequent wheat yields were 3245 kg/ha. In contrast, after two susceptible crops, e.g. wheat followed by soybean, P. thornei populations were 10 850/kg soil and subsequent wheat yields were just 1383 kg/ha. Regression analysis showed a linear, negative response of wheat biomass and grain yield with increasing P. thornei populations and a predicted loss of 77% for biomass and 62% for grain yield. The best predictor of wheat yield loss was P. thornei populations at 0-90 cm soil depth. Crop rotation can be used to reduce P. thornei populations and increase wheat yield, with greatest gains being made following two partially resistant crops grown sequentially.

Johnalcornia gen. et. comb. nov., and nine new combinations in Curvularia based on molecular phylogenetic analysis

An examination of ex-type and authentic cultures of 34 species of Bipolaris and Curvularia by phylogenetic analysis of four loci (EF-1α, GAPDH, ITS and LSU) resulted in nine new combinations in Curvularia, as well as new synonymies for some species of Bipolaris and Curvularia. Lectotypes are designated for Bipolaris secalis and Curvularia richardiae, and an epitype is designated for Curvularia crustacea. A new monotypic genus, Johnalcornia, is introduced to accommodate Bipolaris aberrans, which clusters sister to the newly described Porocercospora. Johnalcornia differs morphologically from this taxon by producing distinctive conidia-like chlamydospores as well as comparatively thick-walled, geniculate conidiophores, with conidiogenous cells that have conspicuous scars. Johnalcornia further differs from related genera by forming the second conidial septum in the apical cell.

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.

Veneer Grade Analysis of Early to Mid-rotation Plantation Eucalyptus Species in Australia

Processing Australian hardwood plantations into rotary veneer can produce more acceptable marketable product recoveries compared to traditional processing techniques (e.g. sawmilling). Veneers resulting from processing trials from six commercially important Australian hardwood species were dominated by D-grade veneer. Defects such as encased knots, gum pockets, gum veins, surface roughness, splits, bark pockets, and decay impacted the final assigned grade. Four grading scenarios were adopted. The first included a change to the grade limitations for gum pockets and gum veins, while the second investigated the potential impact of effective pruning on grade recovery. Although both scenarios individually had a positive impact on achieving higher face grade veneer qualities, the third and fourth scenarios, which combined both, had a substantial impact, with relative veneer values increasing up to 18.2% using conservative calculations (scenario three) or up to 22.6% (scenario four) where some of the upgraded veneers were further upgraded to A-grade, which attracts superior value. The total change in veneer value was found to depend on the average billet diameter unless defects other than those relating to the scenarios (gum or knots) restricted the benefit of pruning and gum upgrading. This was the case for species prone to high levels of growth stress and related defects.

Diagnostic Molecular Markers for Phosphine Resistance in U.S. Populations of Tribolium castaneum and Rhyzopertha dominica

Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T.castaneum and R.dominica with strong resistance was identified as P45S in T.castaneum and P49S in R.dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T.castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

Molecular evidence of Ebola Reston virus infection in Philippine bats

Background: In 2008-09, evidence of Reston ebolavirus (RESTV) infection was found in domestic pigs and pig workers in the Philippines. With species of bats having been shown to be the cryptic reservoir of filoviruses elsewhere, the Philippine government, in conjunction with the Food and Agriculture Organization of the United Nations, assembled a multi-disciplinary and multi-institutional team to investigate Philippine bats as the possible reservoir of RESTV. Methods: The team undertook surveillance of bat populations at multiple locations during 2010 using both serology and molecular assays. Results: A total of 464 bats from 21 species were sampled. We found both molecular and serologic evidence of RESTV infection in multiple bat species. RNA was detected with quantitative PCR (qPCR) in oropharyngeal swabs taken from Miniopterus schreibersii, with three samples yielding a product on conventional hemi-nested PCR whose sequences differed from a Philippine pig isolate by a single nucleotide. Uncorroborated qPCR detections may indicate RESTV nucleic acid in several additional bat species (M. australis, C. brachyotis and Ch. plicata). We also detected anti-RESTV antibodies in three bats (Acerodon jubatus) using both Western blot and ELISA. Conclusions: The findings suggest that ebolavirus infection is taxonomically widespread in Philippine bats, but the evident low prevalence and low viral load warrants expanded surveillance to elaborate the findings, and more broadly, to determine the taxonomic and geographic occurrence of ebolaviruses in bats in the region. © 2015 Jayme et al.

Soybean rotation and crop residue management to reduce nitrous oxide emissions from sugarcane soils

NITROUS OXIDE (N2O) IS a potent greenhouse gas and the predominant ozone-depleting substance in the atmosphere. Agricultural nitrogenous fertiliser use is the major source of human-induced N2O emissions. A field experiment was conducted at Bundaberg from October 2012 to September 2014 to examine the impacts of legume crop (soybean) rotation as an alternative nitrogen (N) source on N2O emissions during the fallow period and to investigate low-emission soybean residue management practices. An automatic monitoring system and manual gas sampling chambers were used to measure greenhouse gas emissions from soil. Soybean cropping during the fallow period reduced N2O emissions compared to the bare fallow. Based on the N content in the soybean crop residues, the fertiliser N application rate was reduced by about 120 kg N/ha for the subsequent sugarcane crop. Consequently, emissions of N2O during the sugarcane cropping season were significantly lower from the soybean cropped soil than those from the conventionally fertilised (145 kg N/ha) soil following bare fallow. However, tillage that incorporated the soybean crop residues into soil promoted N2O emissions in the first two months. Spraying a nitrification inhibitor (DMPP) onto the soybean crop residues before tillage effectively prevented the N2O emission spikes. Compared to conventional tillage, practising no-till with or without growing a nitrogen catch crop during the time after soybean harvest and before cane planting also reduced N2O emissions substantially. These results demonstrated that soybean rotation during the fallow period followed with N conservation management practices could offer a promising N2O mitigation strategy in sugarcane farming. Further investigation is required to provide guidance on N and water management following soybean fallow to maintain sugar productivity.

A molecular survey of Eimeria in chickens across Australia

Coccidiosis is a costly enteric disease of chickens caused by protozoan parasites of the genus Eimeria. Disease diagnosis and management is complicated since there are multiple Eimeria species infecting chickens and mixed species infections are common. Current control measures are only partially effective and this, combined with concerns over vaccine efficacy and increasing drug resistance, demonstrates a need for improved coccidiosis diagnosis and control. Before improvements can be made, it is important to understand the species commonly infecting poultry flocks in both backyard and commercial enterprises. The aim of this project was to conduct a survey and assessment of poultry Eimeria across Australia using genetic markers, and create a collection of isolates for each Eimeria species. A total of 260 samples (faecal or caecal) was obtained, and survey results showed that Eimeria taxa were present in 98% of commercial and 81% of backyard flocks. The distribution of each Eimeria species was widespread across Australia, with representatives of all species being found in every state and territory, and the Eimeria species predominating in commercial flocks differed from those in backyard flocks. Three operational taxonomic units also occurred frequently in commercial flocks highlighting the need to understand the impact of these uncharacterised species on poultry production. As Eimeria infections were also frequent in backyard flocks, there is a potential for backyard flocks to act as reservoirs for disease, especially as the industry moves towards free range production systems. This Eimeria collection will be an important genetic resource which is the crucial first step in the development of more sophisticated diagnostic tools and the development of new live vaccines which ultimately will provide savings to the industry in terms of more efficient coccidiosis management.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.