Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Distribution of barnacle epizoites of the crab Portunus pelagicus in the Moreton Bay region, eastern Australia

The parasites of some decapod crustaceans are known to cause sterilisation of their hosts, and can thus have an important impact on the population dynamics of infested species. Blue swimmer crabs (Portunus pelagicus) collected in three areas around Moreton Bay, Australia were examined for the presence of epizoic barnacles in their branchial chambers and on their carapace. Of the 952 crabs inspected 92% were infested with Octolasmis spp. The mean number of barnacles (predominantly Octolasmis warwickii) per carapace and gill chamber (mainly O. angulata) were 2.35 and 71.1, respectively. Barnacle infestation of gills was found to differ significantly by area, season and sex with the deeper offshore areas exhibiting the highest number of barnacles. The distribution within the hosts showed barnacles were more likely to be distributed in areas closer to the inhalant aperture. Highest abundances were found on the proximal surface of the hypobranchial side of gills 3, 4 and 5. Host moult stage and parasitism by Sacculina granifera were also found to affect the abundance of epizoic barnacles in some areas.

High resolution genetic and physical mapping of the I-3 region of tomato chromosome 7 reveals almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with duplications on Arabidopsis chromosomes 1, 2 and 3

The tomato I-3 gene introgressed from the Lycopersicon pennellii accession LA716 confers resistance to race 3 of the fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici. We have improved the high-resolution map of the I-3 region of tomato chromosome 7 with the development and mapping of 31 new PCR-based markers. Recombinants recovered from L. esculentum cv. M82 × IL7-2 F2 and (IL7-2 × IL7-4) × M82 TC1F2 mapping populations, together with recombinants recovered from a previous M82 × IL7-3 F2 mapping population, were used to position these markers. A significantly higher recombination frequency was observed in the (IL7-2 × IL7-4) × M82 TC1F2 mapping population based on a reconstituted L. pennellii chromosome 7 compared to the other two mapping populations based on smaller segments of L. pennellii chromosome 7. A BAC contig consisting of L. esculentum cv. Heinz 1706 BACs covering the I-3 region has also been established. The new high-resolution map places the I-3 gene within a 0.38 cM interval between the molecular markers RGA332 and bP23/gPT with an estimated physical size of 50-60 kb. The I-3 region was found to display almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with Arabidopsis thaliana chromosomes 1, 2 and 3. An S-receptor-like kinase gene family present in the I-3 region of tomato chromosome 7 was found to be present in the microsyntenous region of grape chromosome 12 but was absent altogether from the A. thaliana genome.

The distribution of Fasciola hepatica in Queensland, Australia, and the potential impact of introduced snail intermediate hosts

A survey was conducted to establish the distribution of the liver fluke, Fasciola hepatica, in the state of Queensland, Australia, and to evaluate the impact of the introduced snail intermediate hosts, Pseudosuccinia columella and Austropeplea viridis. Serum samples from a total of 5103 homebred cattle in 142 beef herds distributed throughout the state and 523 pooled milk samples from dairy herds from the state's major dairying regions were tested for antibodies to F. hepatica by ELISA. Snails were collected on infected properties around the limits of the F. hepatica distribution. F. hepatica infection was detected in 44 dairy herds and two beef herds. The distribution of infected herds indicates that F. hepatica is established only in southeast Queensland. The distribution there was patchy but the parasite was more widespread than suggested by an earlier survey. The predominant intermediate host species found along the northern limit of the distribution was P. columella. We conclude that the introduction of P. columella and A. viridis has not yet had a major impact on the distribution of F. hepatica in Queensland. However, the presence of P. columella, which is much more adaptable to tropical habitats than the native intermediate host, Austropeplea tomentosa, at the northern limit of the F. hepatica distribution suggests that there is potential for the parasite to expand its range.

Genetic erosion and changes in distribution of sorghum (Sorghum bicolor L. (Moench)) landraces in north-eastern Ethiopia

Ethiopia is believed to be the centre of origin and domestication for sorghum, where sorghum remains one of the main staple crops. Loss of biodiversity is occurring at an alarming rate in Ethiopia and crops, including sorghum, have long been recognized as vulnerable to genetic erosion. A major collection of sorghum germplasm was made in 1973 by Gebrekidan and Ejeta from north-eastern Ethiopia. A new collection of landraces was made in 2003, and these were field evaluated at Sirinka in 2004 along with representative samples from the 1973 collection. Farmer surveys and soil and climate surveys were also performed. Preliminary analysis demonstrated that some important landraces have disappeared either locally or regionally in the past 30 years and many other landraces have become marginalized. Landraces which are less preferred in terms of agronomic value and end use, and introductions, have become increasingly important. Late maturing landraces were found to be particularly vulnerable, with a number disappearing altogether. Farmers have become more risk averse, and factors such as declining soil fertility, more frequent drought and unreliable rainfall, and increased pest infestation have contributed to a change in farmer landrace selection. Data are presented on the variability and unique characters of some of the Ethiopian landraces, and implications for conservation are discussed.

The potential geographic distribution of the invasive weed Senna obtusifolia in Australia

Senna obtusifolia (sicklepod) is an invasive weed of northern Australia, where it significantly impacts agricultural productivity and alters natural ecosystem structure and function. Although currently restricted to northern regions, the potential for S. obtusifolia to spread south is not known. Using the eco-climatic model CLIMEX, this study simulated the potential geographic distribution of S. obtusifolia in Australia under two scenarios. Model parameters for both scenarios were derived from the distribution of S. obtusifolia throughout North and Central America. The first scenario used these base model parameters to predict the distribution of S. obtusifolia in Australia, whilst the second model predicted the distribution of a cold susceptible S. obtusifolia ecotype that is reported to occur in the USA. Both models predicted the potential for an extensive S. obtusifolia distribution, with the first model indicating suitable climatic conditions occurring predominantly in coastal regions from the Northern Territory, to far north Queensland and into northern Victoria. The cold susceptible ecotype displayed a comparatively reduced distribution in the southern parts of Australia, where inappropriate temperatures, a lack of thermal accumulation and cold stress restrict the invasion south to the coastal regions of central New South Wales. The extent of the predicted distribution of both ecotypes of S. obtusifolia reinforces the need for strategic management at a national scale.

Is the distribution of Fiji leaf gall in Australian sugarcane explained by variation in the vector Perkinsiella saccharicida?

Fiji leaf gall (FLG) is an important virally induced disease in Australian sugarcane. It is confined to southern canegrowing areas, despite its vector, the delphacid planthopper Perkinsiella saccharicida, occurring in all canegrowing areas of Queensland and New South Wales. This disparity between distributions could be a result of successful containment of the disease through quarantine and/or geographical barriers, or because northern Queensland populations of Perkinsiella may be poorer vectors of the disease. These hypotheses were first tested by investigating variation in the ITS2 region of the rDNA fragment among eastern Australian and overseas populations of Perkinsiella. The ITS2 sequences of the Western Australian P. thompsoni and the Fijian P. vitiensis were distinguishable from those of P. saccharicida and there was no significant variation among the 26 P. saccharicida populations. Reciprocal crosses of a northern Queensland and a southern Queensland population of P. saccharicida were fertile, so they may well be conspecific. Single vector transmission experiments showed that a population of P. saccharicida from northern Queensland had a higher vector competency than either of two southern Queensland populations. The frequency of virus acquisition in the vector populations was demonstrated to be important in the vector competency of the planthopper. The proportion of infected vectors that transmitted the virus to plants was not significantly different among the populations tested. This study shows that the absence of FLG from northern Queensland is not due to a lack of vector competency of the northern population of P. saccharicida.

The distribution of badnavirus-infected Musa germplasm from the International Transit Centre, Katholieke Universiteit Leuven, Belgium

Bioversity International is reviewing its moratorium on the distribution of virus-infected Musa germplasm from the International Transit Centre (ITC), and the ProMusa Crop Protection Working Group has been invited to comment on policy changes. This paper was written to form a basis of discussion among the working group members during the ISHS/ProMusa symposium. It argues that the distribution of Musa germplasm should be guided by the International Plant Protection Convention, which states that it is the responsibility of the importing country, not the exporter, to impose the phytosanitary measures. There may be special circumstances where the release of badnavirus-infected germplasm from the ITC could be justified.

Factors affecting localized abundance and distribution of lesser mealworm in earth-floor broiler houses in subtropical Australia.

Factors that influence the localized abundance and distribution of lesser mealworm, Alphitobius diaperinus (Panzer), in litter of two compacted earth-floor broiler houses in subtropical Australia were studied using various experimental manipulations. Numbers of lesser mealworms substantially increased inside caged areas and under uncaged empty feed pans placed in open areas of the houses. These populations were found to be localized and independent of chicken-feed, manure, and high beetle populations that normally occur under existing feed pans. Substantial horizontal movement of larvae to under feed pans was recorded. Placing metal barriers around these pans significantly restricted this movement. In almost all treatments, lesser mealworms typically peaked in numbers during the middle of the flock time. This temporal pattern of abundance also was observed under pans within barriers, where relatively low insect numbers occurred, but it was not observed in uncaged open areas (where chickens had complete access). It is likely that larvae do not establish in open areas, but fluctuate in numbers as they either move to refuges away from chickens or suffer high rates of mortality. In these refuges, larvae peak in numbers and then leave the litter environment to pupate in the earth floor before the end of the flock time. This behavior might be exploited for management of lesser mealworm by targeting applications of control agents.

Thermal tolerance and potential distribution of Carvalhotingis visenda (Hemiptera: Tingidae), a biological control agent for cat's claw creeper, Macfadyena unguis-cati (Bignoniaceae)

The specialist tingid, Carvalhotingis visenda, is a biological control agent for cat's claw creeper, Macfadyena unguis-cati (Bignoniaceae). Cat's claw creeper is an invasive liana with a wide climatic tolerance, and for biological control to be effective the tingid must survive and develop over a range of temperatures. We evaluated the effect of constant temperatures (0-45°C) on the survival and development of C. visenda. Adults showed tolerance for wider temperature ranges (0-45°C), but oviposition, egg hatching and nymphal development were all affected by both high (>30°C) and low (<20°C) temperatures. Temperatures between 20°C and 30°C are the most favourable for adult survival, oviposition, egg hatching and nymphal development. The ability of adults and nymphs to survive for a few days at high (40°C and 45°C) and low (0°C and 5°C) temperatures suggest that extreme temperature events, which usually occur for short durations (hours) in cat's claw creeper infested regions in Queensland and New South Wales states are not likely to affect the tingid population. The potential number of generations (egg to adult) the tingid can complete in a year in Australia ranged from three to eight, with more generations in Queensland than in New South Wales.

Fencing artificial waterpoints failed to influence density and distribution of red kangaroos (Macropus rufus)

Provision of artificial waterpoints in Australian rangelands has resulted in an increase in the range and density of kangaroos. At high densities, kangaroos can inhibit vegetation regeneration, particularly in some protected areas where harvesting is prohibited. Fencing off waterpoints has been proposed to limit these impacts. Our aim was to determine whether fencing off waterpoints during a drought (when kangaroos would be especially water-limited) would influence the density and distribution of red kangaroos (Macropus rufus). Two waterpoints were fenced within the first 6 months of the 27-month study and a further two waterpoints were kept unfenced as controls in Idalia National Park, western Queensland. We estimated kangaroo densities around waterpoints from walked line-transect counts, and their grazing distribution from dung-pellet counts. Fencing off waterpoints failed to influence either the density or distribution up to 4 km from the waterpoints. Our results indicate that food availability, rather than the location of waterpoints, determines kangaroo distribution. Few areas in the rangelands are beyond kangaroos' convenient reach from permanent waterpoints. Therefore, fencing off waterpoints without explicitly considering the spatial context in relation to other available water sources will fail to achieve vegetation regeneration.

Allocasuarina tree hosts determine the spatial distribution of hypogeous fungal sporocarps in three tropical Australian sclerophyll forests

Across three tropical Australian sclerophyll forest types, site-specific environmental variables could explain the distribution of both quantity (abundance and biomass) and richness (genus and species) of hypogeous fungi sporocarps. Quantity was significantly higher in the Allocasuarina forest sites that had high soil nitrogen but low phosphorous. Three genera of hypogeous fungi were found exclusively in Allocasuarina forest sites including Gummiglobus, Labyrinthomyces and Octaviania, as were some species of Castoreum, Chondrogaster, Endogone, Hysterangium and Russula. However, the forest types did not all group according to site-scale variables and subsequently the taxonomic assemblages were not significantly different between the three forest types. At site scale, significant negative relationships were found between phosphorous concentration and the quantity of hypogeous fungi sporocarps. Using a multivariate information theoretic approach, there were other more plausible models to explain the patterns of sporocarp richness. Both the mean number of fungal genera and species increased with the number of Allocasuarina stems, at the same time decreasing with the number of Eucalyptus stems. The optimal conditions for promoting hypogeous fungi sporocarp quantity and sporocarp richness appear to be related to the presence and abundance of Allocasuarina (Casuarinaceae) host trees. Allocasuarina tree species may have a higher host receptivity for ectomycorrhizal hypogeous fungi species that provide an important food resource for Australian mycophagous animals.

The Distribution of Henipaviruses in Southeast Asia and Australasia: Is Wallace's Line a Barrier to Nipah Virus?

Nipah virus (NiV) (Genus Henipavirus) is a recently emerged zoonotic virus that causes severe disease in humans and has been found in bats of the genus Pteropus. Whilst NiV has not been detected in Australia, evidence for NiV-infection has been found in pteropid bats in some of Australia's closest neighbours. The aim of this study was to determine the occurrence of henipaviruses in fruit bat (Family Pteropodidae) populations to the north of Australia. In particular we tested the hypothesis that Nipah virus is restricted to west of Wallace's Line. Fruit bats from Australia, Papua New Guinea, East Timor and Indonesia were tested for the presence of antibodies to Hendra virus (HeV) and Nipah virus, and tested for the presence of HeV, NiV or henipavirus RNA by PCR. Evidence was found for the presence of Nipah virus in both Pteropus vampyrus and Rousettus amplexicaudatus populations from East Timor. Serology and PCR also suggested the presence of a henipavirus that was neither HeV nor NiV in Pteropus alecto and Acerodon celebensis. The results demonstrate the presence of NiV in the fruit bat populations on the eastern side of Wallace's Line and within 500 km of Australia. They indicate the presence of non-NiV, non-HeV henipaviruses in fruit bat populations of Sulawesi and Sumba and possibly in Papua New Guinea. It appears that NiV is present where P. vampyrus occurs, such as in the fruit bat populations of Timor, but where this bat species is absent other henipaviruses may be present, as on Sulawesi and Sumba. Evidence was obtained for the presence henipaviruses in the non-Pteropid species R. amplexicaudatus and in A. celebensis. The findings of this work fill some gaps in knowledge in geographical and species distribution of henipaviruses in Australasia which will contribute to planning of risk management and surveillance activities.

Alginate encapsulation of shoot tips and nodal segments for short-term storage and distribution of the eucalypt Corymbia torelliana × C. citriodora

A protocol was developed for short-term preservation and distribution of the plantation eucalypt, Corymbia torelliana × C. citriodora, using alginate-encapsulated shoot tips and nodes as synthetic seeds. Effects of sowing medium, auxin concentration, storage temperature and planting substrate on shoot regrowth or conversion into plantlets were assessed for four different clones. High frequencies of shoot regrowth (76–100%) from encapsulated explants were consistently obtained in hormone-free half- and full-strength Murashige and Skoog (MS) sowing media. Conversion into plantlets from synthetic seeds was achieved on half-strength MS medium by treating shoot tips or nodes with 4.9–78.4 μM IBA prior to encapsulation. Pre-treatment with 19.6 μM IBA provided 62–100% conversion, and 95–100% of plantlets survived after acclimatisation under nursery conditions. Synthetic seeds containing explants pre-treated with IBA were stored for 8 weeks much more effectively at 25°C than at 4°C, with regrowth frequencies of 50–84% at 25°C compared with 0–4% at 4°C. To eliminate the in vitro culture step after encapsulation, synthetic seeds were allowed to pre-convert before sowing directly onto a range of ex vitro non-sterile planting substrates. Highest frequencies (46–90%) of plantlet formation from pre-converted synthetic seeds were obtained by transferring shoot tip-derived synthetic seeds onto an organic compost substrate. These plantlets exhibited almost 100% survival in the nursery without mist irrigation. Pre-conversion of non-embryonic synthetic seeds is a novel technique that provides a convenient alternative to somatic embryo-derived artificial seeds.