NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

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.

Can soil nematode community structure be used to indicate soil carbon dynamics in horticultural systems?

There is a need to develop indicators that relate the dynamics of soil organic carbon (SOC) with changes in land management of horticultural production systems. Soil nematode communities have been shown to be sensitive to land management changes, but often do not include plant-parasites in the calculation of soil nematode community indices. The concept of nematode functional guilds was used to estimate the proportion of carbon entering the soil ecosystem through different channels, such as through decomposition of organic material, the detrital channel, through the roots of plants, the root channel or recycled through the activity of predators, a predation channel. Calculations of the indices were developed and validated using case studies in the north Queensland banana industry. Firstly, a survey of organic and conventional banana farms found a greater proportion of C entering the soil ecosystem through the detrital channel and a reduced proportion of C originating through the root channel at the organic sites relative to conventional sites. Secondly, a field experiment comparing compost amendments, found application of fresh compost significantly increased the proportion of C entering the soil ecosystem through the detrital channel and decreased proportion of C originating from the root channel. Thirdly, a field experiment comparing 'conventional' banana production to an 'alternative' system which incorporated organic matter, found the proportion of C entering the soil ecosystem through the root channel was significantly greater in the conventional systems relative to the alternative system. This research demonstrates that nematode indices can be used to assess horticultural systems, by indicating the origins of SOC.

Ground cover management alters development of Fusarium wilt symptoms in Ducasse bananas

Many banana producing regions around the world experience climate variability as a result of seasonal rainfall and temperature conditions, which result in sub-optimal conditions for banana production. This can create periods of plant stress which impact on plant growth, development and yields. Furthermore, diseases such as Fusarium wilt caused by Fusarium oxysporum f. sp. cubense, can become more predominant following periods of environmental stress, particularly for many culturally significant cultivars such as Ducasse (synonym Pisang Awak) (Musa ABB). The aim of this experiment was to determine if expression of symptoms of Fusarium wilt of bananas in a susceptible cultivar could be explained by environmental conditions, and if soil management could reduce the impact of the disease and increase production. An experiment was established in an abandoned commercial field of Ducasse bananas with a high incidence of Fusarium wilt. Vegetated ground cover was maintained around the base of banana plants and compared with plants grown in bare soil for changes in growth, production and disease symptoms. Expression of Fusarium wilt was found to be a function of water stress potential and the heat unit requirement for bananas. The inclusion of vegetative ground cover around the base of the banana plants significantly reduced the severity and incidence of Fusarium wilt by 20 % and altered the periods of symptom development. The growth of bananas and development of the bunch followed the accumulated heat units, with a greater number of bunched plants evident during warmer periods of the year. The weight of bunches harvested in a second crop cycle was increased when banana plants were grown in areas with vegetative ground cover, with fewer losses of plants due to Fusarium wilt.

Planet of the cavendish - understanding the domination

Those seeking to bring change to cultivars sold in the banana markets of the world have encountered major difficulties over the years. Change has been sought because of production difficulties caused by banana diseases such as Fusarium wilt or a desire to invigorate a stagnant market and obtain a competitive advantage by the introduction of diversity of product. Currently the world banana scene is dominated by cultivars from the Cavendish subgroup with their production in excess of 40% of total world production of banana and plantain combined, and in most western countries Cavendish is synonymous with banana. But Cavendish production usually necessitates very regular applications of pesticides, particularly fungicides for Mycosphaerella leaf spots control. So genetic resistance to these and other diseases would be very beneficial to minimizing costs of production, as well as reducing health risks to banana workers and the general population and minimizing impacts on the environment. In recent years, the overall market sales of some crops, such as tomatoes, have increased by providing diversity of cultivars to consumers. Can the same be done for banana? Perhaps a better understanding of how we have arrived at our current situation and the forces that have shaped our preference for Cavendish will allow us to plan more strategic crop improvement research which has enhanced chances of adoption by the banana industries of the world. A scoping study was recently undertaken in Australia to determine the current market opportunity for alternative cultivars and provide a roadmap for the industry to successfully develop this market. A multidisciplinary team reviewed the literature, surveyed the supply chain, analyzed gross margins and conducted consumer and sensory evaluations of 'new' cultivars. This has provided insight on why Cavendish dominates the market, which is the focus of this paper, and we believe will provide a solid foundation for future progress.

Phytochemicals in Japanese plums: impact of maturity and bioaccessibility

In recent years there has been increasing consumer interest in the potential health benefits of dietary derived phytochemicals such as polyphenols (including anthocyanins and flavonols) and carotenoids. A new variety of Japanese plum (Prunus salicina Lindl.), named Queen Garnet (QG), was developed as a high anthocyanin plum in a Queensland (Australia) Government breeding program and may be attractive to consumers, but knowledge of other phytochemical content, and bioaccessibility, is currently limited. As a result, the present study examined (1) the impact of harvest date on anthocyanins, quercetin glycosides and carotenoids in Queen Garnet and another red fleshed commercial Japanese plum variety, Black Diamond (BD), (2) the content of bound phenolics in plum fruit and (3) the in vitro bioaccessibility and release of these phytochemicals as an initial measure to predict their potential bioavailability. For both QG and BD, the last harvest resulted in the highest anthocyanin content in peel, flesh and whole fruit, whereas no significant effects could be observed for quercetin glycosides, and total carotenoids decreased over time. The highest content of bound phenolics (30% of total amount) could be found in BD flesh. Between 53% and 59% of quercetin glycosides and anthocyanins were released from QG after the gastric and small intestinal digestion procedure, whereas the release of carotenoids ranged between 4–6%. A relative high release of anthocyanins and quercetin glycosides could be observed from QG which may result in a higher gastro-intestinal absorption rate of these compounds. However, follow-up studies (clinical trials) are warranted to investigate the in vivo bioavailability and subsequently biological activity of QG.

Polyphenolic contents and the effects of methanol extracts from mango varieties on breast cancer cells

Bioactivities of peel and flesh extracts of 3 genetically diverse mango (Mangifera indica L.) varieties were studied. Nam Doc Mai peel extracts, containing the largest amounts of polyphenols, were associated with an effect on MCF-7 viable cell numbers with an IC50 (dose required for 50% inhibition of cell viability) of 56 μg/mL and significantly (p<0.01) induced cell death in MDA-MB-231 cells, compared with other varieties. Hydrophilic fractions of Nam Doc Mai peel extracts had the highest bioactivity values against both MCF-7 and MDA-MB-231 cells. Soluble polyphenols were present in the largest amounts in most hydrophilic fractions. The Nam Doc Mai mango variety contains high levels of fruit peel bioactivity, which appears to be related to the nature of the polyphenol composition.

Continuous combined microwave and hot air treatment of apples for fruit fly (Bactrocera tryoni and B. jarvisi) disinfestation

Apples at 24 ± 2 °C were heated in a pilot scale hot air assisted (40 °C) continuous pentagonal microwave system, to evaluate the effectiveness of this treatment on insect mortality (variety Mutsu) and fruit quality (variety Granny Smith). An average temperature of 53.4 ± 1.3 °C at core, bottom and flesh of the apple was recorded at the end of the treatment. One hundred percent mortality of the most tolerant stage of Queensland fruit fly (Bactrocera tryoni, Froggatt) and Jarvis's fruit fly (Bactrocera jarvisi, Tryon), were observed when the Mortality value (M52, equivalent time of isothermal treatment at 52 °C) at the slowest heating point applicable for each experiment was ≥ 50 min and ≥ 37 min, respectively. Results showed that microwave heat treatment is effective for insect disinfestation without any adverse impact on total soluble solids, flesh or peel firmness of the treated apples. The treated apples recorded a significantly higher pH and lower ion leakage than the untreated apples after 3 or 4 weeks. Therefore, the microwave heat treatment has the potential to be developed as an alternative chemical free quarantine treatment against economically significant insect pests. Industrial relevance Hot air assisted microwave heating of fruits and vegetables, is more cost effective compared to vapour heat treatment and ionising radiation for disinfestation of insects. Microwave treatment is environmentally friendly compared to fumigation and chemical treatments. Hot air assisted microwave disinfestation can be performed at farms or centralised pack houses since the capital cost would be comparatively lower than vapour heat or ionising radiation treatments.

Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties

Background: Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles. Results: A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316bp. Variety IW had the highest SNP frequency (one SNP every 258bp) while KP and NDM had similar frequencies (one SNP every 369bp and 360bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3'-hydroxylase (F3'H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties. Conclusions: The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango. © 2015 Hoang et al.

Biological data and model development for management of longfinned eels

Objectives: 1. Estimate population parameters required for a management model. These include survival, density, age structure, growth, age and size at maturity and at recruitment to the adult eel fishery. Estimate their variability among individuals in a range of habitats. 2. Develop a management population dynamics model and use it to investigate management options. 3. Establish baseline data and sustainability indicators for long-term monitoring. 4. Assess the applicability of the above techniques to other eel fisheries in Australia, in collaboration with NSW. Distribute developed tools via the Australia and New Zealand Eel Reference Group.

Evaluation of chlorothalonil and paraffinic oil alone and in combinations with registered fungicides for the control of yellow Sigatoka (Mycosphaerella musicola) of bananas in Northern Queensland, Australia

The efficacy of chlorothalonil and paraffinic oil alone and in combinations with the registered fungicides propiconazole, tebuconazole, difenoconazole, epoxiconazole and pyrimethanil was evaluated in a field experiment over two cropping cycles in 2013 and 2014 in Northern Queensland, Australia, for control of yellow Sigatoka (caused by Mycosphaerella musicola) of banana. The predominantly applied by the banana industry treatment mancozeb with paraffinic oil was included for comparison. The results from the two cropping cycles suggested that all chemicals used with paraffinic oil were as effective or more effective than when applied with chlorothalonil, and chlorothalonil alone. Difenoconazole and epoxiconazole with paraffinic oil followed by propiconazole with paraffinic oil were the most effective treatments. Pyrimethanil and tebuconazole plus chlorothalonil were the least effective treatments. None of the chemical treatments was phytotoxic or reduced yield.