Center for Tropical Agriculture

Mareeba, Australia

Center for Tropical Agriculture

Mareeba, Australia

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Karan M.,Center for Tropical Agriculture | Evans D.S.,Center for Tropical Agriculture | Reilly D.,Australian Department of Primary Industries and Fisheries | Schulte K.,Australian Tropical Herbarium | And 3 more authors.
Molecular Ecology Resources | Year: 2012

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. © 2011 Blackwell Publishing Ltd.


Miyata S.,Japan National Agriculture and Food Research Organization | Kato H.,Japan National Agriculture and Food Research Organization | Davis R.,Northern Australia Quarantine Strategy | Smith M.W.,Bundaberg Research Station | And 2 more authors.
Journal of General Plant Pathology | Year: 2011

'Candidatus Liberibacter asiaticus' is the most widespread of the three species of 'Ca. Liberibacter' that cause citrus greening disease (huanglongbing). To ascertain the phylogenetic relationships among Indian isolates that have higher diversity in the 16S rDNA than Asian isolates of this species, we collected symptomatic leaves from Northeast India, Papua New Guinea and Timor-Leste (East Timor) and detected 'Ca. L. asiaticus' by PCR using primers specific for nusG-rplK genes and 16S rDNA. Phylogenetic analysis with 16S rDNA sequences and single nucleotide polymorphisms of the omp gene region revealed that the Northeast Indian isolates were genetically closer to Asian-common isolates from Japan, Taiwan, and Vietnam than to Indian isolates reported previously. Thus, the Asian-common strains of 'Ca. L. asiaticus' are apparently also present in Northeast India. © 2010 The Phytopathological Society of Japan and Springer.


Katoh H.,Japan National Agriculture and Food Research Organization | Davis R.,Northern Australia Quarantine Strategy | Smith M.W.,Bundaberg Research Station | Weinert M.,Center for Tropical Agriculture | Iwanami T.,Japan National Agriculture and Food Research Organization
Annals of Applied Biology | Year: 2012

Japanese isolates of 'Candidatus Liberibacter asiaticus' have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole-genome sequence and were used to differentiate non-Japanese samples of 'Ca. Liberibacter asiaticus' (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived. © 2012 Association of Applied Biologists.


Cogle A.L.,Center for Tropical Agriculture | Cogle A.L.,Khan Research Laboratories | Keating M.A.,Center for Tropical Agriculture | Langford P.A.,Center for Tropical Agriculture | And 2 more authors.
Soil Research | Year: 2011

Runoff, soil loss, and nutrient loss were assessed on a Red Ferrosol in tropical Australia over 3 years. The experiment was conducted using bounded, 100-m2 field plots cropped to peanuts, maize, or grass. A bare plot, without cover or crop, was also instigated as an extreme treatment. Results showed the importance of cover in reducing runoff, soil loss, and nutrient loss from these soils. Runoff ranged from 13% of incident rainfall for the conventional cultivation to 29% under bare conditions during the highest rainfall year, and was well correlated with event rainfall and rainfall energy. Soil loss ranged from 30t/ha.year under bare conditions to <6t/ha.year under cropping. Nutrient losses of 35kg N and 35kgP/ha.year under bare conditions and 17kg N and 11kgP/ha.year under cropping were measured. Soil carbon analyses showed a relationship with treatment runoff, suggesting that soil properties influenced the rainfall runoff response. The cropping systems model PERFECT was calibrated using runoff, soil loss, and soil water data. Runoff and soil loss showed good agreement with observed data in the calibration, and soil water and yield had reasonable agreement. Long-term runs using historical weather data showed the episodic nature of runoff and soil loss events in this region and emphasise the need to manage land using protective measures such as conservation cropping practices. Farmers involved in related, action-learning activities wished to incorporate conservation cropping findings into their systems but also needed clear production benefits to hasten practice change. © CSIRO 2011.


Vawdrey L.L.,Center for Wet Tropics Agriculture | Male M.,PO Box 482 | Grice K.R.E.,Center for Tropical Agriculture
Crop Protection | Year: 2015

Results from the first of two artificially inoculated field experiments showed foliar applications of copper hydroxide (Blue Shield Copper) at 600g a.i./100L-1 (0% infected fruit), copper hydroxide+metalaxyl-M (Ridomil Gold Plus.) at 877.5g a.i./100L-1 (0.27%), metiram+pyraclostrobin (Aero) at 720g a.i./100L-1 (0.51%), chlorothalonil (Bravo WeatherStik) at 994g a.i./100L-1 (0.63%) and cuprous oxide (Nordox 750 WG) at 990g a.i./100L-1 (0.8%) of water significantly reduced the percentage of infected fruit compared to potassium phosphonate (Agri-Fos 600) at 1200g a.i./100L-1 (8.22%), dimethomorph (Acrobat) at 108g a.i./100L-1 (11.18%) and the untreated control (16%). Results from the second experiment showed fruit sprayed with copper hydroxide (Champ Dry Prill) at 300 (2.0% infected fruit), 375 (0.4%) and 450g a.i./100L-1 (0.6%) and metiram+pyraclostrobin (Aero) at 360 (2.8%), 480 (0.6%) and 600g a.i./100L-1 of water (1.0%) significantly reduced the percentage of infected fruit compared to the untreated control (19.4%). Foliar sprays of copper hydroxide at 375g a.i./100L-1 in rotation with chlorothalonil at 994g a.i./100L-1 every two weeks is now recommended to growers for controlling Phytophthora fruit rot of papaya. © 2014.


Jones L.M.,Northern Australia Quarantine Strategy NAQS | Grice K.R.E.,Center for Tropical Agriculture | Davis R.I.,Northern Australia Quarantine Strategy NAQS
Australasian Plant Pathology | Year: 2010

Five pathogen-host leaf tissue combinations were used to determine whether dried plant disease material(γ) irradiated at a level of 25 kGy retains diagnostic value when subjected to selected polymerase chain reaction-based assays. Diagnostic amplification of nucleic acids from all anticipated positive samples was successful following γ irradiation. Variability in results is discussed in relation to sample handling. © Australasian Plant Pathology Society 2010.


Dillon N.L.,Center for Tropical Agriculture | Bally I.S.E.,Center for Tropical Agriculture | Wright C.L.,Center for Tropical Agriculture | Hucks L.,Center for Tropical Agriculture | And 2 more authors.
Scientia Horticulturae | Year: 2013

Assessment of genetic diversity is an essential component in germplasm characterisation and utilisation. In this study the genetic diversity of mango was determined among 254 Mangifera indica L. accessions and related Mangifera species originating from 12 diverse geographic areas using eleven known simple sequence repeat (SSR) markers from mango. A total of 133 alleles were detected, ranging from eight (LMMA12) to 16 (MIAC-5) alleles per locus with a mean value of 12.36 and an average polymorphism information content (PIC) of 0.72. The mean number of alleles (8.45) was highest in the South East Asian accessions (Indonesia/Malesia) and lowest in the accessions from the Philippines (2.55). Diversity analysis divided the accessions into four major nodes broadly representing their geographical origins. The genetic diversity of 'Kensington Pride' was confirmed as being very low and no parents for this cultivar were identified. No association could be established between SSR markers analysed and embryony. Ten synonymous accessions were identified with matching genetic identity with at least one other accession at all SSR loci examined. Twenty-two unique genotypes were identified for 50 trees previously assigned different accession names. The remaining accessions were genetically distinct from each other. This increased understanding of genetic diversity in the Australian National Mango Genebank will assist breeders to better select parents with the potential to contribute desired genes to the progeny and thus more rapidly deliver improved cultivars to industry to meet consumer demand. © 2012.


Hardner C.M.,University of Queensland | Wright C.,Agri Science Queensland | Bally I.,Center for Tropical Agriculture
Acta Horticulturae | Year: 2013

Fruit weight is considered an important factor determining consumer choice in mango and other fruit. In this study, breeding values for average fruit weight were predicted for 29 parents and their ancestors from a seedling progeny trial established in northern Queensland using multivariate linear mixed model approaches that incorporated a pedigree. The trial was conducted over 6 seasons from 1999/2000 to 2005/2006 assessing average fruit weight in 1615 progeny (an average of 433 progeny per season) from 40 families made up of 29 cultivar combinations. Different means, breeding values and residual effects were estimated for each season using a factor analytic approach. Average fruit weights were not significantly different among seasons, however, there was a significant (p = 0.003) effect of year of planting. Additive genetic effects were large with average narrow sense heritability of 0.79. Family effects were very small and not significant. Breeding values were very strongly correlated among seasons (rg = 0.98), however, there was no strong correlation in non-genetic effects on the average fruit weight of progeny among seasons (re = 0.29) suggesting that environmental impacts on average fruit weight may differ between years. The estimated breeding values indicated that on average, progeny from crosses with the cultivars 'Keitt' and 'Kent' produced the largest fruit and progeny from 'Creeping' and 'Williard' produced the smallest fruit. Implications for mango breeding are discussed. © ISHS 2013.


Richards A.E.,CSIRO | Brackin R.,University of Queensland | Lindsay D.A.J.,Center for Tropical Agriculture | Schmidt S.,University of Queensland
Austral Ecology | Year: 2012

Fire is an important driver of nutrient cycling in savannas. Here, we determined the impact of fire frequency on total and soluble soil nitrogen (N) pools in tropical savanna. The study sites consisted of 1-ha experimental plots near Darwin, Australia, which remained unburnt for at least 14years or were burnt at 1-, 2- or 5-year intervals over the past 6years. Soil was analysed from patches underneath tree canopies and in inter-canopy patches at 1, 12, 28, 55 and 152days after fire. Patch type had a significant effect on all soil N pools, with greater concentrations of total and soluble (nitrate, ammonium, amino acids) N under tree canopies than inter-canopy patches. The 'time since the last fire' had no significant effect on N pools. Fire frequency similarly did not affect total soil N but it did influence soluble soil N. Soil amino acids were most prominent in burnt savanna, ammonium was highest in infrequently burnt (5-year interval) savanna and nitrate was highest in unburnt savanna. We suggest that the main effect of fire on soil N relations occurs indirectly through altered tree-grass dynamics. Previous studies have shown that high fire frequencies reduce tree cover by lowering recruitment and increasing mortality. Our findings suggest that these changes in tree cover could result in a 30% reduction in total soil N and 10-60% reductions in soluble N pools. This finding is consistent with studies from savannas globally, providing further evidence for a general theory of patchiness as a key driver of nutrient cycling in the savanna biome. © 2012 Ecological Society of Australia.


Fruit drop can cause major yield losses in Australian lychee orchards, the severity varying with cultivar and season. Research in China, South Africa and Israel has demonstrated the potential for synthetic auxins used as foliar sprays to reduce fruit drop in lychee. Trials tested the efficacy of the synthetic auxin 3-5-6 trichloro-2-phridyl-oxyacetic acid (TPA) applied as a foliar spray at 50 ppm on fruit drop and fruit size on the cultivars 'Fay Zee Siu', 'Kaimana', 'Kwai Mai Pink', 'Souey Tung' and 'Tai So'. TPA reduced fruit drop when applied to fruit greater than 12 mm in length but increased fruit drop when fruit were smaller. Fruit size at the time of application had less effect on the response than the level of natural fruit drop. When natural fruit drop was high, TPA significantly reduced it; by up to 18.7% in 'Fay Zee Siu', 37.1% in 'Kaimana', 39.8% in 'Kwai Mai Pink', 15.1% in 'Souey Tung' and 7.7% in 'Tai So'. TPA was less effective when natural fruit drop was low. TPA increased the number of large fruit and frequently increased the number of small fruit at harvest. The small fruit were associated with an increase in the retention of fruit with poorly developed (chicken tongue) seed. Average fruit size was generally larger (up to 12.7% in 'Souey Tung' and 22% in 'Tai So') with TPA applications.

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