ORCID Profile
0000-0002-7935-6151
Current Organisation
Alkahest Inc
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Population, Ecological and Evolutionary Genetics | Conservation and Biodiversity | Biogeography and Phylogeography | Genetics
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Environmental Sciences | Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Related Links
Publications
Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype
Publisher: The Royal Society
Date: 25-02-2009
Abstract: Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic ersity may be scale dependent.
Transcriptional variation is associated with differences in shoot sodium accumulation in distinct barley varieties
Publisher: Elsevier BV
Date: 10-2019
LNISKS: Reference-free mutation identification for large and complex crop genomes
Publisher: Cold Spring Harbor Laboratory
Date: 19-03-2019
DOI: 10.1101/580829
Abstract: Mutation discovery is often key to the identification of genes responsible for major phenotypic traits. In the context of 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 ergent from the studied accession. Reference-free methods based on short sequences of length k ( k -mers), such as NIKS, exploit redundancy of information across pools of recombinant genomes. Building on concepts from NIKS we introduce LNISKS, a mutation discovery method which is suited for large and repetitive crop genomes. In our experiments, it rapidly and with high confidence, identified mutations from over 700 Gbp of bread wheat genomic sequence data. LNISKS is publicly available at suchecki/LNISKS .
Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank
Publisher: MDPI AG
Date: 21-12-2021
Abstract: Rusts and powdery mildew are diseases that have a major effect on yield loss in barley. Adult Plant Resistance (APR) is a post-seedling resistance mechanism and its expression is influenced by many factors, including host susceptibility and weather conditions, as well as the timing and severity of disease outbreaks. There are two mechanisms associated with APR: non-hypersensitive and minor gene APR. In this study, 431 European barley accessions were evaluated phenotypically over 2 years (2018–2019) under field conditions, scoring APR to powdery mildew (PM), barley brown rust (BBR), and stem rust (SR), and genotypically using DArTseq. Accessions were grouped into sub-collections by cultivation period (group A—cultivated prior 1985, B—cultivated after 1985, and C—Polish landraces) and by European country of origin or European region. GWAS was conducted for PM, BBR, and SR, and scored at the heading (HA) and milky-waxy (MW) seed stages in 2019 and maximum scores across all replicates were obtained 2018–2019. Disease severity was sufficient to differentiate the collection according to cultivation time and country of origin and to determine SNPs. Overall, the GWAS analysis identified 73 marker–trait associations (MTAs) with these traits. For PM resistance, we identified five MTAs at both the HA stage and when considering the maximal disease score across both growth stages and both years. One marker (3432490-28-T/C) was shared between these two traits it is located on chromosome 4H. For BBR resistance, six MTAs at HA and one MTA at the MW stage in 2019 and seven MTAs, when considering the maximal disease score across both growth stages and both years, were identified. Of the 48 markers identified as being associated with SR resistance, 12 were on chromosome 7H, 1 was in the telomeric region of the short arm, and 7 were in the telomeric region of the long arm. Rpg1 has previously been mapped to 7HS. The results of this study will be used to create a Polish Gene Bank platform for precise breeding programs. The resistant genotypes and MTA markers will serve as a valuable resource for breeding for PM, BBR, and SR resistance in barley.
Transient treatment of pregnant Merino ewes with modulators of cortisol biosynthesis coinciding with primary wool follicle initiation alters lifetime wool growth
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/AN12193
Abstract: The economically important characteristics of the adult fleece of Merino sheep, such as increases in clean fleece weight, fibre length, fibre diameter and crimp characteristics are determined during critical phases of fetal development of the skin and its appendages. Genetics plays a major role in the development of traits, but the maternal uterine environment could also influence development. Treatment of pregnant ewes with cortisol and its analogues has previously been shown to produce changes in wool follicle morphology. The aim of this study was to determine the effect of transient manipulation of maternal cortisol status during critical phases of wool follicle initiation and development in utero. From Days 55–65 post-conception, singleton-bearing Merino ewes were treated with metyrapone (cortisol inhibitor) or betamethasone (cortisol analogue). Lambs exposed to metyrapone in utero were born with hairier birthcoats than the control or betamethasone treatment groups (P 0.05), displayed a 10% increase in staple length and a reduction in crimp frequency for the first three shearings (P 0.05). Co-expression network analysis of microarray data revealed up-regulation of members of the transforming growth factor-β and chemokine receptor superfamilies, gene families known to influence hair and skin development. These experiments demonstrate that presumptive transient manipulation of maternal cortisol status coinciding with the initiation of fetal wool follicle development results in long-term alteration in fleece characteristics, namely fibre length and fibre crimp frequency. These results indicate it is possible to alter the lifetime wool production of Merino sheep with therapeutics targeted to gene expression during key windows of development in utero.
Best practice data life cycle approaches for the life sciences
Publisher: F1000 Research Ltd
Date: 04-06-2018
DOI: 10.12688/F1000RESEARCH.12344.2
Abstract: Throughout history, the life sciences have been revolutionised by technological advances in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
SAI: Fast and automated quantification of stomatal parameters on microscope images
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2022
DOI: 10.1101/2022.02.07.479482
Abstract: Using microscopy to investigate stomatal behaviour is a common technique in plant physiology research. Manual inspection and measurement of stomatal features is a low throughput process in terms of time and human effort, which relies on expert knowledge to identify and measure stomata accurately. This process represents a significant bottleneck in research pipelines, adding significant researcher time to any project that requires it. To alleviate this, we introduce StomaAI (SAI): a reliable and user-friendly tool that measures stomata of the model plant Arabidopsis (dicot) and the crop plant barley (monocot grass) via the application of deep computer vision. We evaluated the reliability of predicted measurements: SAI is capable of producing measurements consistent with human experts and successfully reproduced conclusions of published datasets. Hence, SAI boosts the number of images that biologists can evaluate in a fraction of the time so is capable of obtaining more accurate and representative results.
SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
Publisher: Oxford University Press (OUP)
Date: 11-06-2012
DOI: 10.1093/NAR/GKS561
Genetic architecture of gene expression in ovine skeletal muscle
Publisher: Springer Science and Business Media LLC
Date: 12-2011
Abstract: In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this genetic merit are largely undefined. Genetic variation within a population has potential, amongst other mechanisms, to alter gene expression via cis- or trans-acting mechanisms in a manner that impacts the functional activities of specific pathways that contribute to muscling traits. By integrating sire-based genetic merit information for a muscling trait with progeny-based gene expression data we directly tested the hypothesis that there is genetic structure in the gene expression program in ovine skeletal muscle. The genetic performance of six sires for a well defined muscling trait, longissimus lumborum muscle depth, was measured using extensive progeny testing and expressed as an Estimated Breeding Value by comparison with contemporary sires. Microarray gene expression data were obtained for longissimus lumborum s les taken from forty progeny of the six sires (4-8 progeny/sire). Initial unsupervised hierarchical clustering analysis revealed strong genetic architecture to the gene expression data, which also discriminated the sire-based Estimated Breeding Value for the trait. An integrated systems biology approach was then used to identify the major functional pathways contributing to the genetics of enhanced muscling by using both Estimated Breeding Value weighted gene co-expression network analysis and a differential gene co-expression network analysis. The modules of genes revealed by these analyses were enriched for a number of functional terms summarised as muscle sarcomere organisation and development, protein catabolism (proteosome), RNA processing, mitochondrial function and transcriptional regulation. This study has revealed strong genetic structure in the gene expression program within ovine longissimus lumborum muscle. The balance between muscle protein synthesis, at the levels of both transcription and translation control, and protein catabolism mediated by regulated proteolysis is likely to be the primary determinant of the genetic merit for the muscling trait in this sheep population. There is also evidence that high genetic merit for muscling is associated with a fibre type shift toward fast glycolytic fibres. This study provides insight into mechanisms, presumably subject to strong artificial selection, that underpin enhanced muscling in sheep populations.
POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat
Publisher: Springer Science and Business Media LLC
Date: 30-10-2017
DOI: 10.1038/S41598-017-14591-7
Abstract: 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 is achieved by leveraging several of the most commonly used data sets in wheat research. These include the Chromosome Survey Sequences, their order along the chromosomes determined by the population sequencing (POPSEQ) approach, the gene predictions and RNA-Seq expression data. POTAGE aggregates those data sets and provides an intuitive interface for biologists to explore the expression of the predicted genes and their functional annotation in a chromosomal context. The interface accelerates some of the laborious and repetitive tasks commonly undertaken in the process of identifying and prioritising genes which may underlie QTL. We illustrate the utility of POTAGE by showing how a short-list of candidate genes can quickly be identified for a QTL linked to pre-harvest sprouting - a major cause of quality and yield loss in wheat production. The candidate genes identified using POTAGE included TaMKK3 , which was recently reported as a causal gene for seed dormancy in wheat, and a mutation in its barley ortholog has been shown to reduce pre-harvest sprouting. POTAGE is available at crobiad.agwine.adelaide.edu.au otage .
A single nucleotide polymorphism in an IgA1 protease gene determines Streptococcus pneumoniae adaptation to the middle ear during otitis media.
Publisher: Oxford University Press (OUP)
Date: 10-12-2021
Abstract: Factors facilitating the chronicity of otitis media (OM) in children are, to date, not fully understood. An understanding of molecular factors aiding bacterial persistence within the middle ear during OM could reveal pathways required for disease. This study performed a detailed analysis of Streptococcus pneumoniae populations isolated from the nasopharynx and middle ear of one OM case. Isolates were assessed for growth in vitro and infection in a mouse intranasal challenge model. Whole genome sequencing was performed to compare the nasopharyngeal and middle ear isolates. The middle ear isolate displayed a reduced rate of growth and enhanced potential to transit to the middle ear in a murine model. The middle ear population possessed a single nucleotide polymorphism (SNP) in the IgA1 protease gene igA, predicted to render its product non-functional. Allelic exchange mutagenesis of the igA alleles from the genetic variant middle ear and nasopharyngeal isolates was able to reverse the niche-adaptation phenotype in the murine model. These results indicate the potential role of a SNP in the gene encoding the IgA1 protease, in determining S. pneumoniae adaptation to the middle ear during chronic OM. In contrast, a functional IgA1 protease was associated with increased colonisation of the nasopharynx.
Genetic architecture of gene expression in the chicken
Publisher: Springer Science and Business Media LLC
Date: 2013
Back matter
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1MB90044G
Fructilactobacillus cliffordii sp. nov., Fructilactobacillus hinvesii sp. nov., Fructilactobacillus myrtifloralis sp. nov., Fructilactobacillus carniphilus sp. nov. and Fructobacillus americanaquae sp
Publisher: Microbiology Society
Date: 16-02-2023
Abstract: Six strains, KI11_D11 T , KI4_B1, KI11_C11 T , KI16_H9 T , KI4_A6 T and KI3_B9 T , were isolated from insects and flowers on Kangaroo Island, South Australia. On the basis of 16S rRNA gene phylogeny, strains KI11_D11 T , KI4_B1, KI11_C11 T , KI16_H9 T , KI4_A6 T were found to be closely related to Fructilactobacillus ixorae Ru20-1 T . Due to the lack of a whole genome sequence for this species, whole genome sequencing of Fructilactobacillus ixorae Ru20-1 T was undertaken. KI3_B9 T was found to be closely related to Fructobacillus tropaeoli F214-1 T . Utilizing core gene phylogenetics and whole genome analyses, such as determination of AAI, ANI and dDDH, we propose that these six isolates represent five novel species with the names Fructilactobacillus cliffordii (KI11_D11 T = LMG 32130 T = NBRC 114988 T ), Fructilactobacillus hinvesii (KI11_C11 T = LMG 32129 T = NBRC 114987 T ), Fructilactobacillus myrtifloralis (KI16_H9 T = LMG 32131 T = NBRC 114989 T ) Fructilactobacillus carniphilus (KI4_A6 T = LMG 32127 T = NBRC 114985 T ) and Fructobacillus americanaquae (KI3_B9 T = LMG 32124 T = NBRC 114983 T ). Chemotaxonomic analyses detected no fructophilic characters for these strains of member of the genus Fructilactobacillus . KI3_B9 T was found to be obligately fructophilic, similarly to its phylogenetic neighbours in the genus Fructobacillus . This study represents the first isolation, to our knowledge, of novel species in the family Lactobacillaceae from the Australian wild.
The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia
Publisher: Springer Science and Business Media LLC
Date: 25-06-2022
DOI: 10.1038/S41598-022-14893-5
Abstract: Oryza australiensis is a wild rice native to monsoonal northern Australia. The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. Assembly of the O. australiensis genome has previously been challenging due to its high Long Terminal Repeat (LTR) retrotransposon (RT) content. Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. After alignment to the Oryza sativa cv. Nipponbare genome, we observed several structural variations. PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. Although genetic similarity reflected geographical separation, the density of SNVs also correlated with our previous report on variations in salinity tolerance. This genome re-confirms the genetic remoteness of the O. australiensis lineage within the O. officinalis genome complex. Assembly of a high-quality genome for O. australiensis provides an important resource for the discovery of critical genes involved in development and stress tolerance.
Identifying the genetic control of salinity tolerance in the bread wheat landrace Mocho de Espiga Branca
Publisher: CSIRO Publishing
Date: 04-10-2021
DOI: 10.1071/FP21140
Abstract: Salinity tolerance in bread wheat is frequently reported to be associated with low leaf sodium (Na+) concentrations. However, the Portuguese landrace, Mocho de Espiga Branca, accumulates significantly higher leaf Na+ but has comparable salinity tolerance to commercial bread wheat cultivars. To determine the genetic loci associated with the salinity tolerance of this landrace, an F2 mapping population was developed by crossing Mocho de Espiga Branca with the Australian cultivar Gladius. The population was phenotyped for 19 salinity tolerance subtraits using both non-destructive and destructive techniques. Genotyping was performed using genotyping-by-sequencing (GBS). Genomic regions associated with salinity tolerance were detected on chromosomes 1A, 1D, 4B and 5A for the subtraits of relative and absolute growth rate (RGR, AGR respectively), and on chromosome 2A, 2B, 4D and 5D for Na+, potassium (K+) and chloride (Cl−) accumulation. Candidate genes that encode proteins associated with salinity tolerance were identified within the loci including Na+/H+ antiporters, K+ channels, H+-ATPase, calcineurin B-like proteins (CBLs), CBL-interacting protein kinases (CIPKs), calcium dependent protein kinases (CDPKs) and calcium-transporting ATPase. This study provides a new insight into the genetic control of salinity tolerance in a Na+ accumulating bread wheat to assist with the future development of salt tolerant cultivars.
Ten simple rules and a template for creating workflows-as-applications
Publisher: Public Library of Science (PLoS)
Date: 15-12-2022
Genome-wide identification of MicroRNAs in leaves and the developing head of four durum genotypes during water deficit stress
Publisher: Public Library of Science (PLoS)
Date: 12-11-2015
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
Publisher: Springer Science and Business Media LLC
Date: 09-06-2010
Abstract: Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance). The current challenge is that the information holding the clues to SNP functions is distributed across many different databases. Efficient bioinformatics tools are therefore needed to seamlessly integrate up-to-date functional information on SNPs. Many web services have arisen to meet the challenge but most work only within the framework of human medical research. Although we acknowledge the importance of human research, we identify there is a need for SNP annotation tools for other organisms. We introduce an R package called FunctSNP, which is the user interface to custom built species-specific databases. The local relational databases contain SNP data together with functional annotations extracted from online resources. FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies). We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. We illustrate the use of FunctSNP with a livestock ex le, but the approach and software tools presented here can be applied also to human and other organisms. Finding the potential functional significance of SNPs is important when further using the outcomes from whole genome association studies. FunctSNP is unique in that it is the only R package that links SNPs to functional annotation. FunctSNP interfaces to local SNP customised databases which can be built for any species contained in the National Center for Biotechnology Information dbSNP database.
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia
Publisher: Oxford University Press (OUP)
Date: 29-03-2013
DOI: 10.1093/BIB/BBT022
Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops
Publisher: Oxford University Press (OUP)
Date: 16-03-2016
DOI: 10.1093/BIB/BBW013
Development of a cloud-based Bioinformatics Training Platform
Publisher: Oxford University Press (OUP)
Date: 15-04-2017
DOI: 10.1093/BIB/BBW032
DArT-based evaluation of soybean germplasm from Polish Gene Bank
Publisher: Springer Science and Business Media LLC
Date: 30-08-2021
DOI: 10.1186/S13104-021-05750-1
Abstract: Soybean is an important plant used for food, feed and many industrial purposes. Interest in soybean breeding is growing in Central Europe, including Poland. A very large number of soybean accessions are stored in gene banks, but less than 1% of them have been used for breeding. Here, we present genotypic data as well as phenotypic data on plant and seed performance, including seed chlorophyll fluorescence traits, and on yield components within a collection of soybean accessions that are conserved in the Polish Gene Bank at the Plant Breeding and Acclimatization Institute-National Research Institute. The materials used consisted of sub-collections: 79 Polish genotypes, including old traditional cultivars, 24 Canadian, 21 American, 21 Swedish and 31 from Central and Eastern European Countries, 9 from France and 6 from Japan. In total, 9602 high quality SNPs were derived from DArTseq, a method utilising GBS technology. GWAS, performed with the BLINK model, revealed that a total of 41 significant SNPs were mapped for days to flowering, flower colour, plant height, days to pod formation, 100 seed weight, pod colour, seeds and hilum colour and steady-state chlorophyll fluorescence under light (Ft_Lss). This is the first report about the ersity of traditional old Polish soybean cultivars.
gRNA validation for wheat genome editing with the CRISPR-Cas9 system
Publisher: Springer Science and Business Media LLC
Date: 30-10-2019
DOI: 10.1186/S12896-019-0565-Z
Abstract: The CRISPR-Cas9 system is a powerful and versatile tool for crop genome editing. However, achieving highly efficient and specific editing in polyploid species can be a challenge. The efficiency and specificity of the CRISPR-Cas9 system depends critically on the gRNA used. Here, we assessed the activities and specificities of seven gRNAs targeting 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) in hexaploid wheat protoplasts. EPSPS is the biological target of the widely used herbicide glyphosate. The seven gRNAs differed substantially in their on-target activities, with mean indel frequencies ranging from 0% to approximately 20%. There was no obvious correlation between experimentally determined and in silico predicted on-target gRNA activity. The presence of a single mismatch within the seed region of the guide sequence greatly reduced but did not abolish gRNA activity, whereas the presence of an additional mismatch, or the absence of a PAM, all but abolished gRNA activity. Large insertions (≥20 bp) of DNA vector-derived sequence were detected at frequencies up to 8.5% of total indels. One of the gRNAs exhibited several properties that make it potentially suitable for the development of non-transgenic glyphosate resistant wheat. We have established a rapid and reliable method for gRNA validation in hexaploid wheat protoplasts. The method can be used to identify gRNAs that have favourable properties. Our approach is particularly suited to polyploid species, but should be applicable to any plant species amenable to protoplast transformation.
Effects of Rht-B1 and Ppd-D1 loci on pollinator traits in wheat
Publisher: Springer Science and Business Media LLC
Date: 21-03-2019
DOI: 10.1007/S00122-019-03329-W
Abstract: Elite wheat pollinators are critical for successful hybrid breeding. We identified Rht-B1 and Ppd-D1 loci affecting multiple pollinator traits and therefore represent major targets for improving hybrid seed production. Hybrid breeding has a great potential to significantly boost wheat yields. Ideal male pollinators would be taller in stature, contain many spikelets well-spaced along the spike and exhibit high extrusion of large anthers. Most importantly, flowering time would match with that of the female parent. Available genetic resources for developing an elite wheat pollinator are limited, and the genetic basis for many of these traits is largely unknown. Here, we report on the genetic analysis of pollinator traits using biparental mapping populations. We identified two anther extrusion QTLs of medium effect, one on chromosome 1BL and the other on 4BS coinciding with the semi-dwarfing Rht-B1 locus. The effect of Rht-B1 alleles on anther extrusion is genotype dependent, while tall plant Rht-B1a allele is consistently associated with large anthers. Multiple QTLs were identified at the Ppd-D1 locus for anther length, spikelet number and spike length, with the photoperiod-sensitive Ppd-D1b allele associated with favourable pollinator traits in the populations studied. We also demonstrated that homeoloci, Rht-D1 and Ppd-B1, influence anther length among other traits. These results suggest that combinations of Rht-B1 and Ppd-D1 alleles control multiple pollinator traits and should be major targets of hybrid wheat breeding programs.
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
Publisher: Springer Science and Business Media LLC
Date: 17-08-2018
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia
Publisher: Oxford University Press (OUP)
Date: 30-06-2017
DOI: 10.1093/BIB/BBX071
Best Practice Data Life Cycle Approaches for the Life Sciences
Publisher: Cold Spring Harbor Laboratory
Date: 24-07-2017
DOI: 10.1101/167619
Abstract: Throughout history, the life sciences have been revolutionised by technological advances in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C0MB00190B
Abstract: This study reports on the molecular systems biology of gastrointestinal nematode (GIN) infection and potential biomarkers for GIN resistance in sheep. Microarray gene expression data were obtained for 3 different tissues at 4 time points from sheep artificially challenged with two types of nematodes, Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC). We employed an integrated systems biology approach, integrating 3 main methods: standard differential gene expression analyses, weighted gene co-expression network analyses (WGCNA) and quantitative genetic analyses of gene expression traits of key biomarkers. Using standard differential gene expression analyses we identified differentially expressed genes (DE) which responded differently in sheep challenged with HC compared to those challenged with TC. These interaction genes (e.g. MRPL51, SMEK2, CAT, MAPK1IP1 and SLC25A20A) were enriched in Wnt receptor signalling pathway (p = 0.0132) and positive regulation of NFκβ transcription factor activity (p = 0.00208). We report FCER1A, a gene encoding a high-affinity receptor for the Fc region of immunoglobulin E, which is linked to innate immunity to GIN in sheep. Using weighted gene co-expression network analysis (WGCNA) methods, we identified gene modules that were correlated with the length of infection (disease modules). Hub genes (with high intramodular connectivity) were filtered further to identify biomarkers that are related to the length of infection (e.g. CAT, FBX033, COL15A1, IGFBP7, FBLN1 and IgCgamma). The biomarkers we found in HC networks were significantly associated with functions such as T-cell and B-cell regulations, TNF-alpha, interleukin and cytokine production. In TC networks, biomarkers were significantly associated with functions such as protein catabolic process, heat shock protein binding, protein targeting and localization, cytokine receptor binding, TNF receptor binding, apoptosis and IGF binding. These results provide specific gene targets for therapeutic interventions and provide insights into GIN infections in sheep which may be used to infer the same in related host species. This is also the first study to apply the concept of estimating breeding values of animals to expression traits and reveals 11 heritable candidate biomarkers (0.05 to 0.92) that could be used in selection of animals for GIN resistance.
CRISPR/Cas9-mediated knockout of Ms1 enables the rapid generation of male-sterile hexaploid wheat lines for use in hybrid seed production.
Publisher: Wiley
Date: 11-04-2019
DOI: 10.1111/PBI.13106
The Na + transporter, TaHKT1;5-D, limits shoot Na + accumulation in bread wheat
Publisher: Wiley
Date: 10-2014
DOI: 10.1111/TPJ.12651
Abstract: Bread wheat (Triticum aestivum L.) has a major salt tolerance locus, Kna1, responsible for the maintenance of a high cytosolic K(+) /Na(+) ratio in the leaves of salt stressed plants. The Kna1 locus encompasses a large DNA fragment, the distal 14% of chromosome 4DL. Limited recombination has been observed at this locus making it difficult to map genetically and identify the causal gene. Here, we decipher the function of TaHKT1 -D, a candidate gene underlying the Kna1 locus. Transport studies using the heterologous expression systems Saccharomyces cerevisiae and Xenopus laevis oocytes indicated that TaHKT1 -D is a Na(+) -selective transporter. Transient expression in Arabidopsis thaliana mesophyll protoplasts and in situ polymerase chain reaction indicated that TaHKT1 -D is localised on the plasma membrane in the wheat root stele. RNA interference-induced silencing decreased the expression of TaHKT1 -D in transgenic bread wheat lines which led to an increase in the Na(+) concentration in the leaves. This indicates that TaHKT1 -D retrieves Na(+) from the xylem vessels in the root and has an important role in restricting the transport of Na(+) from the root to the leaves in bread wheat. Thus, TaHKT1 -D confers the essential salinity tolerance mechanism in bread wheat associated with the Kna1 locus via shoot Na(+) exclusion and is critical in maintaining a high K(+) /Na(+) ratio in the leaves. These findings show there is potential to increase the salinity tolerance of bread wheat by manipulation of HKT1 genes.
Standard reporting requirements for biological samples in metabolomics experiments: environmental context
Publisher: Springer Science and Business Media LLC
Date: 24-08-2007
AtCIPK16 mediates salt stress through phytohormones and transcription factors
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2020
DOI: 10.1101/2020.02.17.953216
Abstract: Soil salinity causes large productivity losses for agriculture worldwide. “Next-generation crops” that can tolerate salt stress are required for the sustainability of global food production. Previous research in Arabidopsis thaliana aimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16. Overexpression of AtCIPK16 enhanced shoot Na + exclusion and increased biomass in both Arabidopsis and barley. Here, a comparative transcriptomic study on Arabidopsis lines expressing AtCIPK16 was conducted in the presence and absence of salt stress, using an RNA-Seq approach, complemented by AtCIPK16 interaction and localisation studies. We are now able to provide evidence for AtCIPK16 activity in the nucleus. Moreover, the results manifest the involvement of a transcription factor, AtTZF1, phytohormones and the ability to quickly reach homeostasis as components important for improving salinity tolerance in transgenics overexpressing AtCIPK16 . Furthermore, we suggest the possibility of both biotic and abiotic tolerance through AtCIPK16, and propose a model for the salt tolerance pathway elicited through AtCIPK16.
Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial i
Publisher: Microbiology Society
Date: 12-09-2022
Abstract: Four strains, SG5_A10 T , SGEP1_A5 T , SG4_D2 T , and SG4_A1 T , were isolated from the honey or homogenate of Australian stingless bee species Tetragonula carbonaria and Austroplebeia australis . Based on 16S rRNA gene phylogeny, core gene phylogenetics, whole genome analyses such as determination of amino acid identity (AAI), cAAI of conserved genes, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH), chemotaxonomic analyses, and the novel isolation sources and unique geography, we propose three new species and one genus with the names Apilactobacillus apisilvae sp. nov. (SG5_A10 T = LMG 32133 T = NBRC 114991 T ), Bombilactobacillus thymidiniphilus sp. nov. (SG4_A1 T = LMG 32125 T = NBRC 114984 T ), Bombilactobacillus folatiphilus sp. nov. (SG4_D2 T = LMG 32126 T = NBRC 115004 T ) and Nicolia spurrieriana sp. nov. (SGEP1_A5 T = LMG 32134 T = NBRC 114992 T ). Three out of the four strains were found to be fructophilic, where SG5_A10 T and SGEP1_A5 T belong to obligately fructophilic lactic acid bacteria, and SG4_D2 T representing a new type denoted here as kinetically fructophilic. This study represents the first published lactic acid bacterial species associated with the unique niche of Australian stingless bees.
The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance
Publisher: Elsevier BV
Date: 07-2016
DOI: 10.1016/J.YMPEV.2016.03.031
Abstract: Calcineurin B-like protein interacting protein kinases (CIPKs) are key regulators of pre-transcriptional and post-translational responses to abiotic stress. Arabidopsis thaliana CIPK16 (AtCIPK16) was identified from a forward genetic screen as a gene that mediates lower shoot salt accumulation and improved salinity tolerance in Arabidopsis and transgenic barley. Here, we aimed to gain an understanding of the evolution of AtCIPK16, and orthologues of CIPK16 in other plant species including barley, by conducting a phylogenetic analysis of terrestrial plant species. The resulting protein sequence based phylogenetic trees revealed a single clade that included AtCIPK16 along with two segmentally duplicated CIPKs, AtCIPK5 and AtCIPK25. No monocots had proteins that fell into this clade instead the most closely related monocot proteins formed a group basal to the entire CIPK16, 5 and 25 clade. We also found that AtCIPK16 contains a core Brassicales specific indel and a putative nuclear localisation signal, which are synapomorphic characters of CIPK16 genes. In addition, we present a model that proposes the evolution of CIPK16, 5 and 25 clade.
Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko
Publisher: CSIRO Publishing
Date: 2021
DOI: 10.1071/FP20181
Abstract: Hybrid breeding in wheat has the potential to boost yields. An efficient hybrid seed production system requires elite pollinators however, such germplasm is limited among modern cultivars. Piko, a winter wheat (Triticum aestivum L.) cultivar, has been identified as a superior pollinator and has been used in Europe. Piko has favourable pollinator traits for anther extrusion, anther length, pollen mass and hybrid seed set. However, the genetic factors responsible for Piko’s favourable traits are largely unknown. Here, we report on the genetic analysis of a Piko-derived F2 mapping population. We confirmed that Piko’s Rht-D1a allele for tall stature is associated with large anthers and high anther extrusion. However, Rht-D1 was not found to be associated with anther filament length, confirmed by near isogenic lines. Piko’s photoperiod sensitive Ppd-B1b allele shows an association with increased spike length, more spikelets and spike architecture traits, while the insensitive Ppd-B1a allele is linked with high anther extrusion and larger anthers. We identified an anther extrusion quantitative trait locus (QTL) on chromosome 6A that showed significantly biased transmission of the favourable Piko allele amongst F2 progenies. The Piko allele is completely absent in the distal 6AS region and the central 6A region revealed a significantly lower ratio (& %) of F2 with homozygous Piko alleles. Our study provided further evidence for the effects of Rht-D1 and Ppd-B1 loci on multiple pollinator traits and a novel anther extrusion QTL that exhibits segregation distortion.
The complete genome sequence of elite bread wheat cultivar, “Sonmez”
Publisher: F1000 Research Ltd
Date: 06-06-2022
DOI: 10.12688/F1000RESEARCH.121637.1
Abstract: High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low-irrigation conditions, which further improves upon irrigation. Additionally, Sonmez-2001 is resilient against certain biotic stressors, particularly soil-borne pathogens. Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling 13.3 gigabase-pairs in length. Additionally, a de novo assembly of an additional 1.05 gigabase-pairs was generated that represents either Sonmez-specific sequences or sequences that considerably erged between Sonmez and Chinese Spring. Within this de novo assembly, we identified 35 gene models, of which 11 were high-confidence, that may contribute to the favorable traits of this high-performing variety. We identified up to 24 million sequence variants, of which up to 2.4% reside in coding sequences, that can be used to develop molecular markers that should be of immediate use to the cereal community.
Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method
Publisher: Wiley
Date: 11-2008
DOI: 10.1111/J.1755-0998.2008.02190.X
Abstract: We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous lification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.
Wheat ms5 male‐sterility is induced by recessive homoeologous A and D genome non‐specific lipid transfer proteins
Publisher: Wiley
Date: 21-06-2019
DOI: 10.1111/TPJ.14350
Abstract: Nuclear male-sterile mutants with non-conditional, recessive and strictly monogenic inheritance are useful for both hybrid and conventional breeding systems, and have long been a research focus for many crops. In allohexaploid wheat, however, genic redundancy results in rarity of such mutants, with the ethyl methanesulfonate-induced mutant ms5 among the few reported to date. Here, we identify TaMs5 as a glycosylphosphatidylinositol-anchored lipid transfer protein required for normal pollen exine development, and by transgenic complementation demonstrate that TaMs5-A restores fertility to ms5. We show ms5 locates to a centromere-proximal interval and has a sterility inheritance pattern modulated by TaMs5-D but not TaMs5-B. We describe two allelic forms of TaMs5-D, one of which is non-functional and confers mono-factorial inheritance of sterility. The second form is functional but shows incomplete dominance. Consistent with reduced functionality, transcript abundance in developing anthers was found to be lower for TaMs5-D than TaMs5-A. At the 3B homoeolocus, we found only non-functional alleles among 178 erse hexaploid and tetraploid wheats that include landraces and Triticum dicoccoides. Apparent ubiquity of non-functional TaMs5-B alleles suggests loss-of-function arose early in wheat evolution and, therefore, at most knockout of two homoeoloci is required for sterility. This work provides genetic information, resources and tools required for successful implementation of ms5 sterility in breeding systems for bread and durum wheats.
Four simple recommendations to encourage best practices in research software
Publisher: F1000 Research Ltd
Date: 13-06-2017
DOI: 10.12688/F1000RESEARCH.11407.1
Abstract: Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data
Publisher: Biomedical Informatics
Date: 21-09-2012
DAWN: a resource for yielding insights into the diversity among wheat genomes
Publisher: Springer Science and Business Media LLC
Date: 12-2018
Proximity loggers: Data handling and classification for quality control
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2012
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
Publisher: Oxford University Press (OUP)
Date: 09-12-2010
DOI: 10.1093/BIOINFORMATICS/BTP674
Abstract: Summary: We make the PCIT algorithm, used for detecting meaningful gene–gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script. Availability and implementation: Source code and binaries freely available (under GPL-3) for download via CRAN at ackage=PCIT, implemented in R and supported on Linux and MS Windows. Contact: nathan.watson-haigh@csiro.au
StomaAI: an efficient and user‐friendly tool for measurement of stomatal pores and density using deep computer vision
Publisher: Wiley
Date: 18-02-2023
DOI: 10.1111/NPH.18765
Abstract: Using microscopy to investigate stomatal behaviour is common in plant physiology research. Manual inspection and measurement of stomatal pore features is low throughput, relies upon expert knowledge to record stomatal features accurately, requires significant researcher time and investment, and can represent a significant bottleneck to research pipelines. To alleviate this, we introduce StomaAI (SAI): a reliable, user‐friendly and adaptable tool for stomatal pore and density measurements via the application of deep computer vision, which has been initially calibrated and deployed for the model plant Arabidopsis (dicot) and the crop plant barley (monocot grass). SAI is capable of producing measurements consistent with human experts and successfully reproduced conclusions of published datasets. SAI boosts the number of images that can be evaluated in a fraction of the time, so can obtain a more accurate representation of stomatal traits than is routine through manual measurement. An online demonstration of SAI is hosted at sai.aiml.team , and the full local application is publicly available for free on GitHub through dynames/sai‐app .
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Related Funding Activities
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100065
Start Date: 2013
End Date: 12-2014
Amount: $370,000.00
Funder: Australian Research Council
View Funded Activity