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.

Five new species of Aptenocanthon Matthews (Coleoptera: Scarabaeidae: Scarabaeinae) from tropical Australia, with notes on distribution

Five new species of the flightless scarabaeine genus Aptenocanthon Matthews are described from northern Australia: jimara sp. nov. from the Northern Territory; kabura sp. nov., wollumbin sp. nov., winyur sp. nov. and speewah sp. nov. from mountains in the wet tropics of northern Queensland. A key is given to the eight species in the genus. A. jimara is the first record of the genus away from the east coast. Biology and distribution are discussed.

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.

A spatially explicit multi-competitor coexistence model of penaeid (shrimp) distribution on the Australian Great Barrier Reef

A spatially explicit multi-competitor coexistence model was developed for meta-populations of prawns (shrimp) occupying habitat patches across the Great Barrier Reef, where dispersal was localised and dispersal rates varied between species. Prawns were modelled as individuals moving to and from patches or cells according to pre-set decision rules. The landscape was simulated as a matrix of cells with each cell having a spatially explicit survival index for each species. Mixed species prawn assemblages moved over this simplified spatially explicit landscape. A low level of chronic random environmental disturbance was assumed (cyclone and tropical storm damage) with additional acute spatially confined disturbance due to commercial trawling, modelled as an increase in mortality affecting inter-specific competition. The general form of the results was for increased disturbance to favour good-colonising "generalist" species at the expense of good-competitor "specialists". Increasing fishing mortality (local patch extinctions) combined with poor colonising ability resulted in low equilibrium abundance for even the best competitor, while in the same circumstances the poorest competitor but best coloniser could have the highest equilibrium abundance. This mimics the switch from high-value prawn species to lower-value prawn species as trawl effort increases, reflected in historic catch and effort logbook data and reported anecdotaly from the north Queensland trawl fleet. To match the observed distribution and behaviour of prawn assemblages, a combination inter-species competition, a spatially explicit landscape, and a defined pattern of disturbance (trawling) was required. Modelling this combination could simulate not only general trends in spatial distribution of each of prawn species but also localised concentrations observed in the survey data

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. II. Distribution and diet

This study used faecal pellets to investigate the broadscale distribution and diet of koalas in the mulgalands biogeographic region of south-west Queensland. Koala distribution was determined by conducting faecal pellet searches within a 30-cm radius of the base of eucalypts on 149 belt transects, located using a multi-scaled stratified sampling design. Cuticular analysis of pellets collected ffom 22 of these sites was conducted to identify the dietary composition of koalas within the region. Our data suggest that koala distribution is concentrated in the northern and more easterly regions of the study area, and appears to be strongly linked with annual rainfall. Over 50% of our koala records were obtained from non-riverine communities, indicating that koalas in the study area are not primarily restricted to riverine communities, as bas frequently been suggested. Cuticular analysis indicates that more than 90% of koala diet within the region consists of five eucalypt species. Our data highlights the importance of residual Tertiary landforms to koala conservation in the region.

Selection and characterisation of two attenuated vaccine lines of Eimeria tenella in Australia

Objective To attenuate two strains of Eimeria tenella by selecting for precocious development and evaluate the strains in characterisation trials and by field evaluation, to choose one precocious line for incorporation into an Australian live coccidiosis vaccine for poultry. Design Two strains from non-commercial flocks were passaged through chickens while selecting for precocious development. Each strain was characterised for drug sensitivity, pathogenicity, protection against homologous and heterologous challenge, and oocyst output in replicated experiments in which the experimental unit was a cage of three birds. Oocyst output and/or body weight gain data collected over a 10 to 12 day period following final inoculation were measured. Feed conversion ratios were also calculated where possible. Results Fifteen passages resulted in prepatent periods reduced by 24 h for the Redlands strain (from 144 h to 120 h)and 23 h for the Darryl strain (from 139 h to 116 h). Characterisation trials demonstrated that each precocious line was significantly less pathogenic than its parent strain and each effectively induced immunity that protected chickens against challenge with both the parent strain and other virulent field strains. Both lines had oocyst outputs that, although significantly reduced relative to the parent strains, remained sufficiently high for commercial vaccine production, and both showed susceptibility to coccidiostats. Conclusion Two attenuated lines have been produced that exhibit the appropriate characteristics for use in an Australian live coccidiosis vaccine.

Distribution and abundance of white grubs (Coleoptera: Scarabaeidae) on groundnut in southern India

Scarab species associated with groundnuts were surveyed in Andhra Pradesh, Karnataka and Tamil Nadu, southern India, between 1995 and 2001. Scarab adults were collected from trees on which they were feeding and/or mating, and larvae (white grubs) from groundnut fields. Holotrichia species, especially H. reynaudi and H. serrata were the major species associated with groundnut. H. reynaudi predominated in the central Deccan area, while H. serrata was most abundant in areas to the south and west. A new, undescribed, Holotrichia species near H. consanguinea was collected south and south-west of Hyderabad in mixed populations with H. reynaudi. However, the full extent of this new species’ distribution remains uncertain. H. rufoflava was rarely associated with groundnut, but was common as an adult at some locations. Other genera encountered during surveys were Anomala, Adoretus, Schizonycha, Autoserica. In survey data, densities of Holotrichia larvae and ‘all other white grubs’ were both very highly correlated with % of damaged groundnut plants. These correlations in combination with concurrent observations of plant damage establish a causal link between white grubs and plant damage and death in southern Indian groundnut. Ranking of preferred host trees for adults were developed from field observations for four Holotrichia species and Schizonycha spp. and will assist grower-initiated surveys of pest occurrence. In combination with insecticide efficacy data published elsewhere, the survey provides the basis for an environmentally friendly and economically viable pest-management system for white grubs on groundnut in southern India.

Yield of synthetic backcross-derived lines in rainfed environments of Australia

Wheat is one of the major food crops in the world. It is Australia's largest crop and most important agricultural commodity. In Australia the crop is grown under rainfed conditions with inherently important regional environmental differences; wheat growing areas are characterized by winter dominant rainfall in southern and western Australia and summer rainfall in northern Australia. Maximizing yield potential across these diverse regions is dependent upon managing, either genetically or agronomically, those factors in the environment that limit yield. The potential of synthetic backcross lines (SBLs) to increase yield in the diverse agroecological zones of Australia was investigated. Significant yield advantages were found for many of the SBLs across diverse environments. Depending on the environment, the yield of the SBLs ranged from 8% to 30% higher than the best local check in Australia. Apart from adaptation to semiarid water stressed conditions, some SBLs were also found to be significantly higher yielding under more optimal (irrigated) conditions. The four testing environments were classified into two groups, with the northern and southern environments being in separate groups. An elite group of SBLs was identified that exhibited broad adaptation across all diverse Australian environments included in this study. Other SBLs showed specific adaptation to either northern or southern Australia. This study showed that SBLs are likely to provide breeders with the opportunity to significantly improve wheat yield beyond what was previously possible in a number of diverse production environments.

Diversity in the sunflower: Puccinia helianthi pathosystem in Australia

Sunflower rust caused by Puccinia helianthi is the most important disease of sunflower in Australia with the potential to cause significant yield losses in susceptible hybrids. Rapid and frequent virulence changes in the rust fungus population limit the effective lifespan of commercial cultivars and impose constant pressure on breeding programs to identify and deploy new sources of resistance. This paper contains a synopsis of virulence data accumulated over 25 years, and more recent studies of genotypic diversity and sexual recombination. We have used this synopsis, generated from both published and unpublished data, to propose the origin, evolution and distribution of new pathotypes of P. helianthi. Virulence surveys revealed that diverse pathotypes of P. helianthi evolve in wild sunflower populations, most likely because sexual recombination and subsequent selection of recombinant pathotypes occurs there. Wild sunflower populations provide a continuum of genetically heterogeneous hosts on which P. helianthi can potentially complete its sexual cycle under suitable environmental conditions. Population genetics analysis of a worldwide collection of P. helianthi indicated that Australian isolates of the pathogen are more diverse than non-Australian isolates. Additionally, the presence of the same pathotype in different genotypic backgrounds supported evidence from virulence data that sexual recombination has occurred in the Australian population of P. helianthi at some time. A primary aim of the work described was to apply our knowledge of pathotype evolution to improve resistance in sunflower to sunflower rust. Molecular markers were identified for a number of previously uncharacterised sunflower rust R-genes. These markers have been used to detect resistance genes in breeding lines and wild sunflower germplasm. A number of virulence loci that do not recombine were identified in P. helianthi. The resistance gene combinations corresponding to these virulence loci are currently being introgressed with breeding lines to generate hybrids with durable resistance to sunflower rust.

DArT markers: Diversity analyses and mapping in Sorghum bicolor

The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. Results: A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. Conclusion: We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Distribution and eradication of an exotic tephritid fruit fly in Australia: Relevance of invasion theory

Data from the eradication of the incursion of Bactrocera papayae Drew and Hancock (Dipt.: Tephritidae) in Australia (1995-1998) are used to assess the significance of various aspects of invasion theory, including the influence of towns on establishment, influence of propagule pressure on the pattern of establishment, and the existence of source-sink dynamics. Because there were no sentinel traps in place, considerable spread had occurred before the eradication campaign started. The distribution of fly density around the epicentre in the town of Cairns and a transect along the main traffic routes to the north and south fitted a Cauchy model with a tail having the same slope as a power model with an exponent of -2.4 extending to 160 km. The Cauchy model indicated that 50% of the flies on the transect would have occurred within 3.2 km of the epicentre, 90% within 13.2 km, and 99% within 60 km. The two major satellites at Mareeba (35 km from the epicentre in Cairns) and Mossman (65 km) were not used for the transect data and had respectively 15 and 30 times the density predicted by the model. The proportion of traps that caught flies (a measure of site occupancy) fell with distance from the epicentre. B. papayae was trapped consistently on only three of the 16 rainforest transects that were surveyed and these were relatively close to urban areas where eradication efforts were intense. Despite there being no eradication effort in the rainforest, the trends to extinction were similar to those in adjacent areas. The strategy of initially concentrating eradication efforts on the core and major satellites while maintaining a quarantine barrier at the airport and the boundaries of the infested area appears to be the key to the containment and rapid eradication of the incursion.

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.

Patterns in the distribution and abundance of female eastern king prawns, Melicertus plebejus (Hess, 1865), capable of spawning and reproductive potential in waters off

Linear mixed models were used to test the null hypothesis that there were no differences between seasons and locations in the reproductive potential of female eastern king prawns, Melicertus plebejus along the east coast of Australia. Three samples were collected in each season between autumn 1991 and winter 1992 (inclusive). Females capable of spawning were found at all locations but proportions were greater in lower than higher latitudes. Females capable of spawning were not found at the southern (highest latitude) most location in all seasons. There was a significant interaction in reproductive potential between seasons and locations suggesting that patterns among seasons differed between locations and vice versa. Reproductive potential was greatest amongst the northern (lower latitudes) most locations and was greatest in autumn at these locations. Seasonal patterns were less pronounced further south (higher latitudes). The length composition of females in catches differed between locations with more larger prawns found in samples from northern locations. The challenge that remains is to quantify the oceanic sources of larvae that contribute to recruitment in each nursery area and the estuarine sources of juveniles that contribute adults back to the effective spawning stock. Maintaining the effective spawning stock and important nursery areas are crucial to the sustainability of this resource.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05-7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

Genetic variation and responses in reproductive performance of sows in lines selected for growth rate under restricted feeding

The objective of this study was to examine genetic changes in reproduction traits in sows (total number born (TNB), number born alive (NBA), average piglet birth weight (ABW) and number of piglets weaned (NW), body weight prior to mating (MW), gestation length (GL) and daily food intake during lactation (DFI)) in lines of Large White pigs divergently selected over 4 years for high and low post-weaning growth rate on a restricted ration. Heritabilities and repeatabilities of the reproduction traits were also determined. The analyses were carried out on 913 litter records using average information-restricted maximum likelihood method applied to single trait animal models. Estimates of heritability for most traits were small, except for ABW (0·33) and MW (0·35). Estimates of repeatability were slightly higher than those of heritability for TNB, NBA and NW, but they were almost identical for ABW, MW, GL and DFI. After 4 years of selection, the high growth line sows had significantly heavier body weight prior to mating and produced significantly more piglets born alive with heavier average birth weight than the low line sows. There were, however, no statistical differences between the selected lines in TNB or NW. The lower food intake of high relative to low line sows during lactation was not significant, indicating that daily food intake differences found between grower pigs in the high and low lines (2·71 v. 2·76 kg/day, s.e.d. 0·024) on ad libitum feeding were not fully expressed in lactating sows. It is concluded that selection for growth rate on the restricted ration resulted in beneficial effects on important measures of reproductive performance of the sows.