Risk assessment for Puccinia psidii becoming established in South Africa

Puccinia psidii, the causal agent of myrtle rust, was first recorded from Latin America more than 100 years ago. It occurs on many native species of Myrtaceae in Latin America and also infects non-native plantation-grown Eucalyptus species in the region. The pathogen has gradually spread to new areas including Australia and most recently South Africa. The aim of this study was to consider the susceptibility of selected Eucalyptus genotypes, particularly those of interest to South African forestry, to infection by P. psidii. In addition, risk maps were compiled based on suitable climatic conditions and the occurrence of potential susceptible tree species. This made it possible to identify the season when P. psidii would be most likely to infect and to define the geographic areas where the rust disease would be most likely to establish in South Africa. As expected, variation in susceptibility was observed between eucalypt genotypes tested. Importantly, species commonly planted in South Africa show good potential for yielding disease-tolerant material for future planting. Myrtle rust is predicted to be more common in spring and summer. Coastal areas, as well as areas in South Africa with subtropical climates, are more conducive to outbreaks of the pathogen.

Spatio-temporal patterns in maturation of the chokka squid (Loligo vulgaris reynaudii) off the coast of South Africa

Knowledge of the temporal and spatial characteristics of chokka squid (Loligo vulgaris reynaudii) biology in South African waters is limited, so the possibility of there being a geographically fragmented stock was examined by investigating the distribution of maturity patterns for the species, covering all known spawning areas and using both historical and recent data. Gonadosomatic indices (GSI) varied between year-round consistency and apparent seasonal peaks in both summer and winter; there was no clear spatial pattern. Monthly percentage maturity provided further evidence for two peak reproductive periods each year, although mature squid were present throughout. Sex ratios demonstrated great variability between different areas and life history stages. Male-biased sex ratios were only apparent on the inshore spawning grounds and ranged between 1.118:1 and 4.267:1. Size at sexual maturity was also seasonal, squid maturing smaller in winter/spring than in summer/autumn. Also, squid in the east matured smaller than squid in the west. Although the results from the present study do not provide conclusive evidence of distinct geographic populations, squid likely spawn over a significantly larger area of the Agulhas Bank than previously estimated, and squid on the west coast of South Africa may return to spawn on the western portion of the Agulhas Bank. It remains likely, however, that the east and west coast populations are a single stock and that migration of juveniles to the west coast and their subsequent return as sub-adults is an integral but non-essential and variable part of the life history.

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.

Phytogeny of the Quambalariaceae fam. nov., including important Eucalyptus pathogens in South Africa and Australia

The genus Quambalaria consists of plant-pathogenic fungi causing disease on leaves and shoots of species of Eucalyptus and its close relative, Corymbia. The phylogenetic relationship of Quambalaria spp., previously classified in genera such as Sporothrix and Ramularia, has never been addressed. It has, however, been suggested that they belong to the basidiomycete orders Exobasidiales or Ustilaginales. The aim of this study was thus to consider the ordinal relationships of Q. eucalypti and Q. pitereka using ribosomal LSU sequences. Sequence data from the ITS nrDNA were used to determine the phylogenetic relationship of the two Quambalaria species together with Fugomyces (= Cerinosterus) cyanescens. In addition to sequence data, the ultrastructure of the septal pores of the species in question was compared. From the LSU sequence data it was concluded that Quambalaria spp. and F. cyanescens form a monophyletic clade in the Microstromatales, an order of the Ustilaginomycetes. Sequences from the ITS region confirmed that Q. pitereka and Q. eucalypti are distinct species. The ex-type isolate of F. cyanescens, together with another isolate from Eucalyptus in Australia, constitute a third species of Quambalaria, Q. cyanescens (de Hoog & G.A. de Vries) Z.W. de Beer, Begerow & R. Bauer comb. nov. Transmission electron-microscopic studies of the septal pores confirm that all three Quambalaria spp. have dolipores with swollen lips, which differ from other members of the Microstromatales (i.e. the Microstromataceae and Volvocisporiaceae) that have simple pores with more or less rounded pore lips. Based on their unique ultrastructural features and the monophyly of the three Quambalaria spp. in the Microstromatales, a new family, Quambalariaceae Z.W. de Beer, Begerow & R. Bauer fam. nov., is described.

Construction of microsatellite linkage maps for Corymbia

The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Resistance to the root-lesion nematode Pratylenchus thornei in wheat landraces and cultivars from the West Asia and North Africa (WANA) region.

Resistance to the root-lesion nematode Pratylenchus thornei was sought in wheat from the West Asia and North Africa (WANA) region in the Watkins Collection (148 bread and 139 durum wheat accessions) and the McIntosh Collection (59 bread and 43 durum wheat accessions). It was considered that landraces from this region, encompassing the centres of origin of wheat and where P. thornei also occurs, could be valuable sources of resistance for use in wheat breeding. Resistance was determined by number of P. thornei/kg soil after the growth of the plants in replicated glasshouse experiments. On average, durum accessions produced significantly lower numbers of P. thornei than bread wheat accessions in both the Watkins and McIntosh Collections. Selected accessions with low P. thornei numbers were re-tested and 13 bread wheat and 10 durum accessions were identified with nematode numbers not significantly different from GS50a, a partially resistant bread wheat line used as a reference standard. These resistant accessions, which originated in Iran, Iraq, Syria, Egypt, Sudan, Morocco, and Tunisia, represent a resource of resistance genes in the primary wheat gene pool, which could be used in Australian wheat breeding programs to reduce the economic loss from P. thornei.

DNA bar-coding reveals source and patterns of Thaumastocoris peregrinus invasions in South Africa and South America.

Thaumastocoris peregrinus is a recently introduced invertebrate pest of non-native Eucalyptus plantations in the Southern Hemisphere. It was first reported from South Africa in 2003 and in Argentina in 2005. Since then, populations have grown explosively and it has attained an almost ubiquitous distribution over several regions in South Africa on 26 Eucalyptus species. Here we address three key questions regarding this invasion, namely whether only one species has been introduced, whether there were single or multiple introductions into South Africa and South America and what the source of the introduction might have been. To answer these questions, bar-coding using mitochondrial DNA (COI) sequence diversity was used to characterise the populations of this insect from Australia, Argentina, Brazil, South Africa and Uruguay. Analyses revealed three cryptic species in Australia, of which only T. peregrinus is represented in South Africa and South America. Thaumastocoris peregrinus populations contained eight haplotypes, with a pairwise nucleotide distance of 0.2-0.9% from seventeen locations in Australia. Three of these haplotypes are shared with populations in South America and South Africa, but the latter regions do not share haplotypes. These data, together with the current distribution of the haplotypes and the known direction of original spread in these regions, suggest that at least three distinct introductions of the insect occurred in South Africa and South America before 2005. The two most common haplotypes in Sydney, one of which was also found in Brisbane, are shared with the non-native regions. Sydney populations of T. peregrinus, which have regularly reached outbreak levels in recent years, might thus have served as source of these three distinct introductions into other regions of the Southern Hemisphere.

Inheritance of resistance to root-lesion nematode (Pratylenchus thornei) in wheat landraces and cultivars from the West Asia and North Africa (WANA) region.

The root-lesion nematode Pratylenchus thornei causes substantial loss to bread wheat production in the northern grain region of Australia and other parts of the world. West Asia and North Africa (WANA) wheat accessions with partial resistance to P. thornei were analysed for mode of inheritance in a half-diallel crossing design of F1 hybrids (10 parents) and F2 populations (7 parents). General combining ability was more important than specific combining ability as indicated by components of variance ratios of 0.93 and 0.95 in diallel ANOVA of the F1 and F2 generations, respectively. General combining ability values of the 'resistant' parents were predictive of the mean nematode numbers of their progeny in crosses with the susceptible Australian cv. Janz at the F1 (R populations showed relatively continuous distributions. Heritability was 0.68 for F2 populations in the half-diallel of resistant parents and 0.82-0.92 for 5 'resistant' parent/Janz doubled-haploid populations (narrow-sense heritability on a line mean basis). The results indicate polygenic inheritance of P. thornei resistance with a minimum of from 2 to 6 genes involved in individual F populations of 5 resistant parents crossed with Janz. Morocco 426 and Iraq 43 appear to be the best of the parents tested for breeding for resistance to P. thornei. None of the P. thornei-resistant WANA accessions was resistant to Pratylenchus neglectus.

Australian monocot-infecting mastrevirus diversity rivals that in Africa

Monocotyledonous plant infecting mastreviruses (family Geminiviridae) have been found in the Old World. The greatest diversity of these viruses has been found in Africa but this may simply reflect the more extensive sampling that has been done there. To provide a better understanding of mastrevirus diversity in Australia. we have sequenced the genomes of 41 virus isolates found in naturalised and native grasses and identified four new species in addition to the four previously characterised species. Two of these species, which were recovered from a single Sporobolus plant, are highly divergent and are most closely related to the African streak viruses. This, coupled with the discovery of divergent dicotyledonous plant infecting mastreviruses in Australia brings into question the hypothesis that mastreviruses may have originated in Africa. We found that the patterns of inter- and intra-species recombination and the recombination hotspots mirror those found in both their African monocot-infecting counterparts and dicot-infecting mastrevirus. (C) 2012 Elsevier B.V. All rights reserved.

Development of cat's claw creeper leaf-tying moth Hypocosmia pyrochroma (Lepidoptera: Pyralidae) at different temperatures: Implications for establishment as a biological control agent in Australia and South Africa

The leaf-tying moth Hypocosmia pyrochroma Jones (Lepidoptera: Pyralidae), a native of sub tropical South America, has been introduced as a biological control agent for cat’s claw creeper, Dolichandra unguis-cati (L.) Lohman (Bignoniaceae), in Australia and South Africa. So far there has been no evidence of its field establishment in either country. A narrow temperature tolerance is a potential limiting factor for the establishment of weed biological control insects in novel habitats. In this study, we evaluated the effect of seven constant temperatures (12–40 °C) on the survival and development of H. pyrochroma in temperature-controlled cabinets. Temperatures between 20 and 30 °C were the most favorable for adult survival, oviposition, egg hatching, and larval and pupal development. Adult survival (12–40 °C) and egg development (15–35 °C) showed tolerance for wider temperature ranges than oviposition, and larval and pupal development, which were all negatively affected by both high (>30 °C) and low (<20 °C) temperatures. The degree-day (DD) requirement to complete a generation was estimated as 877 above a threshold temperature of 12 °C. Based on DD requirements and an obligatory winter diapause of pupae from mid-autumn to mid-spring, the potential number of generations (egg to adult) the leaf-tying moth can complete in a year in Australia or South Africa range from one to three. A climate-matching model predicted that the inland regions of both Australia and South Africa are less favorable for H. pyrochroma than the coastal areas. The study suggested that H. pyrochroma is more likely to establish in the coastal areas of Australia where most of the cat’s claw creeper infestations occur, than in South Africa where most of the cat’s claw creeper infestations are inland.

Development of cat’s claw creeper leaf-tying moth Hypocosmia pyrochroma (Lepidoptera: Pyralidae) at different temperatures: Implications for establishment as a biological control agent in Australia and South Africa

The leaf-tying moth Hypocosmia pyrochroma Jones (Lepidoptera: Pyralidae), a native of sub tropical South America, has been introduced as a biological control agent for cat’s claw creeper, Dolichandra unguis-cati (L.) Lohman (Bignoniaceae), in Australia and South Africa. So far there has been no evidence of its field establishment in either country. A narrow temperature tolerance is a potential limiting factor for the establishment of weed biological control insects in novel habitats. In this study, we evaluated the effect of seven constant temperatures (12–40 °C) on the survival and development of H. pyrochroma in temperature-controlled cabinets. Temperatures between 20 and 30 °C were the most favorable for adult survival, oviposition, egg hatching, and larval and pupal development. Adult survival (12–40 °C) and egg development (15–35 °C) showed tolerance for wider temperature ranges than oviposition, and larval and pupal development, which were all negatively affected by both high (>30 °C) and low (<20 °C) temperatures. The degree-day (DD) requirement to complete a generation was estimated as 877 above a threshold temperature of 12 °C. Based on DD requirements and an obligatory winter diapause of pupae from mid-autumn to mid-spring, the potential number of generations (egg to adult) the leaf-tying moth can complete in a year in Australia or South Africa range from one to three. A climate-matching model predicted that the inland regions of both Australia and South Africa are less favorable for H. pyrochroma than the coastal areas. The study suggested that H. pyrochroma is more likely to establish in the coastal areas of Australia where most of the cat’s claw creeper infestations occur, than in South Africa where most of the cat’s claw creeper infestations are inland.

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.

Population dynamics of Thaumastocoris peregrinus in Eucalyptus plantations of South Africa

Thaumastocoris peregrinus is a sap-sucking insect that infests non-native Eucalyptus plantations in Africa, New Zealand, South America and parts of Southern Europe, in addition to street trees in parts of its native range of Australia. In South Africa, pronounced fluctuations in the population densities have been observed. To characterise spatiotemporal variability in T. peregrinus abundance and the factors that might influence it, we monitored adult population densities at six sites in the main eucalypt growing regions of South Africa. At each site, twenty yellow sticky traps were monitored weekly for 30 months, together with climatic data. We also characterised the influence of temperature on growth and survival experimentally and used this to model how temperature may influence population dynamics. T. peregrinus was present throughout the year at all sites, with annual site-specific peaks in abundance. Peaks occurred during autumn (February-April) for the Pretoria site, summer (November-January) for the Zululand site and spring (August-October) for the Tzaneen, Sabie and Piet Retief monitoring sites. Temperature (both experimental and field-collected), humidity and rainfall were mostly weakly, or not at all, associated with population fluctuations. It is clear that a complex interaction of these and other factors (e.g. host quality) influence population fluctuations in an annual, site specific cycle. The results obtained not only provide insights into the biology of T. peregrinus, but will also be important for future planning of monitoring and control programs using semiochemicals, chemical insecticides or biological control agents. © 2014 Springer-Verlag Berlin Heidelberg.