A5068225528- Wheat and Barley Genetics and Pathology
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Soybean genetics and cultivation
- Genetics and Plant Breeding
- Genetic diversity and population structure
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Research Data Management Practices
- Plant Reproductive Biology
- Genome Rearrangement Algorithms
- Legume Nitrogen Fixing Symbiosis
- Chromosomal and Genetic Variations
- Yeasts and Rust Fungi Studies
- Crop Yield and Soil Fertility
- Plant pathogens and resistance mechanisms
- Plant Disease Resistance and Genetics
- Sugarcane Cultivation and Processing
- Plant Pathogens and Resistance
- Plant Micronutrient Interactions and Effects
- Plant nutrient uptake and metabolism
- Biomedical Text Mining and Ontologies
- Rice Cultivation and Yield Improvement
- Genetic Associations and Epidemiology
- Agricultural pest management studies
Agriculture and Food
2019-2025
Commonwealth Scientific and Industrial Research Organisation
2019-2025
The University of Adelaide
2014-2021
Health Sciences and Nutrition
2019
Australian Centre for Plant Functional Genomics
2014-2017
University of East Anglia
2009-2012
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, is currently responsible for 80% of sugar production worldwide
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does aim to propose new development best practices, but rather provide simple recommendations encourage the adoption of existing practices. Software promote better improves reproducibility reusability research. These are designed around Open Source values, practical suggestions contribute making source code more discoverable,...
Abstract The current rate of yield gain in crops is insufficient to meet the predicted demands. Capturing boost from heterosis one few technologies that offers rapid gain. Hybrids are widely used for cereals, maize and rice, but it has been a challenge develop viable hybrid system bread wheat due genome complexity, which both large hexaploid. Wheat our most grown crop providing 20% calories humans. Here, we describe identification Ms1 , gene proposed use large-scale, low-cost production...
Atmospheric vapor pressure deficit (VPD) is a key component of drought and has strong influence on yields. Whole-plant transpiration rate (TR) response to increasing VPD been linked tolerance in wheat, but because its challenging phenotyping, genetic basis remains unexplored. Further, the control other traits daytime TR such as leaf area, stomata densities – more recently nocturnal unknown. Considering presence wheat phenology genes that can interfere with tolerance, aim this investigation...
Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought low nitrogen supply in bread wheat. Allantoin a key target metabolite for improving homeostasis stress. The allantoin an intermediate the catabolism (components nucleotides) known its housekeeping role (N) recycling also function N transport storage nodulated legumes. was shown to differentially accumulate upon abiotic stress range plant species but little about cereals. To address this, purine catabolic...
As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines [1][2][3].Workflow managers, such as Snakemake [4], Nextflow [5], Cromwell [6] with WDL or CWL [7], empower researchers to build robust that call a series of tools scripts perform bespoke analysis.Workflow enable non-bioinformaticians run published confidence, graphical user interfaces Galaxy [8] BioWorkflow [9] have helped nonbioinformaticians create their own...
Summary Nuclear male‐sterile mutants with non‐conditional, recessive and strictly monogenic inheritance are useful for both hybrid conventional breeding systems, have long been a research focus many crops. In allohexaploid wheat, however, genic redundancy results in rarity of such mutants, the ethyl methanesulfonate‐induced mutant ms5 among few reported to date. Here, we identify TaMs5 as glycosylphosphatidylinositol‐anchored lipid transfer protein required normal pollen exine development,...
Recently, much attention has been devoted to the construction of phylogenetic networks which generalize trees in order accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level-1 networks--a type network slightly more general than a tree--from triplets. Our made publicly available as program LEV1ATHAN. It combines ideas from several known theoretical algorithms tree and reconstruction with two novel subroutines. Namely,...
Multilabeled trees or MUL-trees, for short, are whose leaves labeled by elements of some nonempty finite set X such that more than one leaf may be the same element X. This class includes phylogenetic and tree shapes. MUL-trees arise naturally in, example, biogeography gene evolution studies also in area network reconstruction. In this paper, we introduce novel metrics which used to compare most generalize well-known on These can used, better understand space help visualize collections...
New SNP marker platforms offer the opportunity to investigate relationships between wheat cultivars from different regions and assess mechanism processes that have led adaptation particular production environments. Wheat breeding has a long history in Kazakhstan aim of this study was explore relationship key varieties germplasm programs for other regions. The revealed 5,898 polymorphic markers amongst ten cultivars, which 2,730 were mapped consensus genetic map. Mapped distributed almost...
Abstract Motivation Major advances have been made in the assembly of complex genomes such as wheat. Remaining challenges include linking these new resources to legacy research, well lowering bar entry for members research community who may lack specific bioinformatics skills. Results Pretzel aims solve problems by providing an interactive, online environment data visualisation and analysis which, when loaded with appropriately curated data, can enable researchers no training exploit latest...
Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by lack a reference and large computational requirements analysing these sets. DAWN (Diversity Among Wheat geNomes) integrates from T. Chinese Spring (CS) IWGSC RefSeq v1.0 with public WGS exome 17 62 accessions respectively, enabling researchers breeders alike to investigate genotypic differences between wheat at level chromosomes down individual genes. Using we show...
Wheat (Triticum aestivum L.) productivity is severely reduced by high temperatures. Breeding of heat-tolerant cultivars can be achieved identifying genes controlling physiological and agronomical traits when temperatures occur using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We advanced the positional cloning qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased...
Abstract Non-specific Lipid Transfer Proteins (nsLTPs) are involved in numerous biological processes. To date, only a fraction of wheat ( Triticum aestivum L.) nsLTPs (TaLTPs) have been identified, and even fewer functionally analysed. In this study, the identification, classification, phylogenetic reconstruction, chromosome distribution, functional annotation expression profiles TaLTPs were 461 putative identified from genome classified into five types (1, 2, C, D G). Phylogenetic analysis...
Rusts and powdery mildew are diseases that have a major effect on yield loss in barley. Adult Plant Resistance (APR) is post-seedling resistance mechanism its expression influenced by many factors, including host susceptibility weather conditions, as well the timing severity of disease outbreaks. There two mechanisms associated with APR: non-hypersensitive minor gene APR. In this study, 431 European barley accessions were evaluated phenotypically over 2 years (2018–2019) under field scoring...
POPSEQ Ordered Triticum aestivum Gene Expression (POTAGE) is a web application which accelerates the process of identifying candidate genes for quantitative trait loci (QTL) in hexaploid wheat. This achieved by leveraging several most commonly used data sets wheat research. These include Chromosome Survey Sequences, their order along chromosomes determined population sequencing (POPSEQ) approach, gene predictions and RNA-Seq expression data. POTAGE aggregates those provides an intuitive...
Abstract For over a century, Australian wheat breeders have successfully adapted to broad range of climatic conditions and crop management practices. The OzWheat genome-to-phenome (G2P) platform was established capture this breeding history explore traits, genes, their interactions with the environment enable ongoing research deliver targets for improvement. A panel 285 cultivars landraces were chosen through knowledge pedigrees represent both global diversity historic flow genetic variation...
Soybean is an important plant used for food, feed and many industrial purposes. Interest in soybean breeding growing Central Europe, including Poland. A very large number of accessions are stored gene banks, but less than 1% them have been breeding. Here, we present genotypic data as well phenotypic on seed performance, chlorophyll fluorescence traits, yield components within a collection that conserved the Polish Gene Bank at Plant Breeding Acclimatization Institute-National Research...
Abstract Mutation discovery is often key to the identification of genes responsible for major phenotypic traits. In context bulked segregant analysis, common reference-based computational approaches are not always suitable as they rely on a genome assembly which may be incomplete or highly divergent from studied accession. Reference-free methods based short sequences length k ( -mers), such NIKS, exploit redundancy information across pools recombinant genomes. Building concepts NIKS we...
There is a clear demand for hands-on bioinformatics training. The development of workshop content both time-consuming and expensive. Therefore, enabling trainers to develop workshops in way that facilitates reuse becoming increasingly important. most widespread practice sharing through making PDF, PowerPoint Word documents available online. While this effort be commended, such usually not so easy or repurpose does capture all the information required third party rerun workshop. We present an...
There is a growing trend for releasing bioinformatics workflows as command line applications. This good thing workflow management systems add both functionality and reliability, while interfaces are convenient end users. Developing software in this way considerably faster. However, there many potential pitfalls that developers of tools should avoid. We outline ten simple rules converting manager pipelines into applications, present working examples also function templates using the two most...
Puccinia coronata f. sp. avenae is the causal agent of disease known as crown rust, which represents a bottleneck in oat production worldwide. Characterization pathogen populations often involves race (pathotype) assignments using differential sets, are not uniform across countries. This study compared virulence profiles 25 P. isolates from Australia two host one and United States. These sets were also genotyped diversity arrays technology sequencing technology. Phenotypic genotypic...
Abstract Wheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved identifying genes controlling physiological and agronomical traits with temperature using these to select superior genotypes, but no gene underlying genetic variation for tolerance has previously been described. We completed the positional cloning qYDH.3BL , a quantitative trait locus (QTL) on bread wheat chromosome 3B associated increased yield in hot dry climates. The...