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.

Rapid microsatellite marker development for African mahogany ( Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93943 sequences with an average read length of 234bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.

Collecting banana diversity in eastern Indonesia

Major diseases, including Fusarium wilt tropical race 4, threaten banana production systems worldwide. New sources of genetic resistance are considered necessary in the fight against such diseases. The triangular region of Indonesia taking in Sulawesi, the Maluku Islands and Lesser Sunda Islands was prioritized by the Global Musa Genetic Resources Network, MusaNet for exploration and collecting. It is just east of the Wallace Line, which is recognized as a transition zone for flora in southeast Asia, and had been little explored. Bioversity International funded a team of scientists from Indonesia and Australia to make collecting missions in the triangle in October 2012 and February 2013. Suckers and seeds of 35 promising new accessions were collected. About 90% of these are either wild species or diploid cultivars of more direct use to breeding programs. These were morphologically characterized during the collecting missions and included a set of photographs recommended by Bioversitys Taxonomic Advisory Group. Cigar leaf samples were also collected and sent as fresh samples to the International Banana Genotyping Centre in the Czech Republic. Ploidy and DNA (SSR) genotyping determinations from these samples have been invaluable in quickly interpreting and better appreciating what has been discovered. The new accessions have been grown on at Solok field collection, West Sumatra and will be made available by Indonesia to the international community, including breeding programs, for evaluation and utilization. Information on wild Eumusa prompts a rethinking of the phytogeography of Musa acuminata. The variation within the Australimusa species M. lolodensis highlights the need for broader study of this Musa section. French Plantain-like edible AAs and prospects for the generation of African plantains in the region were identified. The mission indicated existence of local edible ABs in eastern Indonesia in association with balbisiana hybrids origins in the region. Further explorations in the region should add to Musa diversity knowledge.

Alkaloid production by isolates of the sorghum ergot pathogen (Claviceps africana) from Australia and other countries

Isolates of Claviceps africana from Australia, Africa, Asia, and America were tested for the production of dihydroergosine (DHES), and its biogenic precursors dihydroelymoclavine (DHEL) and festuclavine (FEST), in culture. Several growth media were evaluated to optimise alkaloid production with little success. The best of these involved 2-stage culturing on high-sucrose substrate. Australian C. africana isolates varied widely and inconsistently in alkaloid production, with DHES concentrations in mycelium ranging from: <0.1 to 9 mg DHES/kg; <0.1 to 1.6 mg DHEL/kg; and <0.1 to 0.4 mg FEST/kg. In a separate experiment using similar culturing techniques, DHES was produced by 2 of 3 Australian isolates, 1 of 3 USA isolates, 1 of 4 Indian isolates, the sole Puerto Rican isolate, the sole Japanese isolate, but not the sole South African isolate. In this experiment, DHES concentrations detected in mycelium of Australian isolates (0.1-1.0 mg DHES/kg) were of similar magnitude to isolates from other countries (0.2-1.8 mg DHES/kg). Three C. africana isolates, including one that produced only traces of alkaloid in culture after 8 weeks, were inoculated onto panicles of sterile male sorghum plants. After 8 weeks, all 3 isolates produced 10-19 mg DHES/kg in the panicles, demonstrating that the growing plant favoured more consistent alkaloid production than culture medium.

Inventories and significance of the genetic resources of an African mahogany species (Khaya senegalensis (Desr.) A. Juss.) assembled and further developed in Australia.

The forest tree species Khaya senegalensis (Desr.) A. Juss. occurs in a belt across 20 African countries from Senegal-Guinea to Sudan-Uganda where it is a highly important resource. However, it is listed as Vulnerable (IUCN 2015-3). Since introduction in northern Australia around 1959, the species has been planted widely, yielding high-value products. The total area of plantations of the species in Australia exceeds 15,000 ha, mostly planted in the Northern Territory since 2006, and includes substantial areas across 60-70 woodlots and industrial plantations established in north-eastern Queensland since the early-1990s and during 2005-2007 respectively. Collaborative conservation and tree improvement by governments began in the Northern Territory and Queensland in 2001 based on provenance and other trials of the 1960s-1970s. This work has developed a broad base of germplasm in clonal seed orchards, hedge gardens and trials (clone and progeny). Several of the trials were established collaboratively on private land. Since the mid-2000s, commercial growers have introduced large numbers of provenance-bulk and individual-tree seedlots to establish industrial plantations and trials, several of the latter in collaboration with the Queensland Government. Provenance bulks (>140) and families (>400) from 17 African countries are established in Australia, considered the largest genetic base of the species in a single country outside Africa. Recently the annual rate of industrial planting of the species in Australia has declined, and R&D has been suspended by governments and reduced by the private sector. However, new commercial plantings in the Northern Territory and Queensland are proposed. In domesticating a species, the strategic importance of a broad genetic base is well known. The wide range of first- and advanced-generation germplasm of the species established in northern Australia and documented in this paper provides a sound basis for further domestication and industrial plantation and woodlot expansion, when investment conditions are favourable

Survival and Growth of Damara, Dorper, Dorset, Rambouillet, South African Meat Merino First Cross Lambs in Semi Arid Queensland

The recent introduction to Australia of superior sheep meat breeds from South Africa provides a basis for improving the quality and amount of sheep meat grown in Queensland’s semi arid area. Alternatively suitable breeds from existing Australian stocks of dual purpose and traditional terminal meat sheep may bring the desired attributes required by the market place. There has been no critical assessment of sheep meat breeds suitably adapted to the rangeland environment of western Queensland. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia.

The domestication of African mahogany (Khaya senegalensis) in northern Australia.

African mahogany has demonstrated much potential, in many field trials spanning several decades and in furniture manufacturers' evaluations, as a high-value timber species for plantations in northern Australia. It is in the early stages of domestication via a low-intensity, informally-collaborative, mostly-public-sector program of conservation and genetic improvement begun 5 y ago. Silvicultural techniques are being developed through experience in both 'small grower' and larger-scale plantings. See this issue's cover for photographs.

Developing African mahogany (Khaya senegalensis) germplasm and its management for a sustainable forest plantation industry in northern Australia: Progress and needs.

The demonstrated wide adaptability, substantial yield potential and proven timber quality of African mahogany (Khaya senegalensis) from plantings of the late 1960s and early 1970s in northern Australia have led to a resurgence of interest in this high-value species. New plantations or trials have been established in several regions since the early 1990s -in four regions in north Queensland, two in the Northern Territory and one in Western Australia. Overall, more than 1500 ha had been planted by early 2007, and the national annual planting from 2007-2008 as currently planned will exceed 2400 ha. Proceedings of two workshops have summarised information available on the species in northern Australia, and suggested research and development (R&D) needs and directions. After an unsustained first phase of domestication of K. senegalensis in the late 1960s to the early 1970s, a second phase began in northern Australia in 2001 focused on conservation and tree improvement that is expected to provide improved planting stock by 2010. Work on other aspects of domestication is also described in this paper: the current estate and plans for extension; site suitability, soils and nutrition; silviculture and management; productivity; pests and diseases; and log and wood properties of a sample of superior trees from two mature plantations of unselected material near Darwin. Some constraints on sustainable plantation development in all these fields are identified and R&D needs proposed. A sustained R&D effort will require a strategic coordinated approach, cooperative implementation and extra funding. Large gains in plantation profitability can be expected to flow from such inputs.

Influence of cyclonic winds on the performance of hardwood plantations in tropical north Queensland.

Severe Tropical Cyclone Yasi crossed the far north Queensland coast at Mission Beach on February 3rd, 2011, shattering the regions developing hardwood plantation industry. The cyclone’s path covered the primary areas of hardwood and softwood plantations in this region, causing widespread destruction. The extent of cyclone damage, coupled with the weak international economy has resulted in a severe decline in industry confidence for the future of timber plantations in this region. This report reviews the impacts of Severe TC Yasi on the performance of key hardwood plantation species in north Queensland. It summarises the influence of species, genetics, plantation design, management and age on plantation resilience. The information will contribute to a “Best Practice Guide for Timber Plantations in Cyclonic Areas” to be produced by Timber Queensland. This will assist companies with future plantation investment decisions in the tropical cyclone zone. 2 200 trees were assessed, including 44 species at 32 localities located from Daintree to Townsville. Data are also presented for a post-cyclone assessment of 5 900 African mahogany trees on four sites in the Ingham region. A report prepared for the Timber Queensland project: Best Practice Guide for Timber Plantations in Cyclonic Areas.

African mahogany (Khaya senegalensis) plantations in Australia - status, needs and progress

The Australian African mahogany estate comprises over 12,000 ha of industrial plantations, farm-forestry plots and trials, virtually all derived from Africa-sourced wild seed. However, the better trees have given high-value products such as veneers, high-grade boards and award-winning furniture. Collaborative conservation and improvement by the Northern Territory (NT) and Queensland governments since 2000 realised seed orchards, hedge gardens and genetic tests revealing promising clones and families. Private sector R&D since the mid 2000s includes silvicultural-management and wood studies, participatory testing of government material and establishing over 90 African provenances and many single-tree seedlots in multisite provenance and family trials. Recent, mainly public sector research included a 5-agency project of 2009-12 resulting in advanced propagation technologies and greater knowledge of biology, wood properties and processing. Operational priority in the short term should focus on developing seed production areas and ‘rolling front’ clonal seed orchards. R&D priorities should include: developing and implementing a collaborative improvement strategy based on pooled resources; developing non-destructive evaluation of select-tree wood properties, micropropagation (including field testing of material from this source) to ‘industry ready’ and a select-tree index; optimising seed production in orchards; advancing controlled pollination techniques; and maximising benefits from the progeny, clone and provenance trials. Australia leads the world in improvement and ex situ conservation of African mahogany based on the governments’ 13-year program and more recent industry inputs such that accumulated genetic resources total over 120 provenances and many families from 15 of the 19 African countries of its range. Having built valuable genetic resources, expertise, technologies and knowledge, the species is almost ‘industry ready’. The industry will benefit if it exploits the comparative advantage these assets provide. However the status of much of the diverse germplasm introduced since the mid 2000s is uncertain due to changes in ownership. Further, recent reductions of government investment in forestry R&D will be detrimental unless the industry fills the funding gaps. Expansion and sustainability of the embryonic industry must capitalise on past and current R&D, while initiating and sustaining critical new work through all-stakeholder collaboration.