ORCID Profile
0000-0003-4018-0694
Current Organisations
The New Zealand Institute for Plant & Food Research Limited
,
New Zealand Institute for Plant and Food Research Ltd
,
University of Otago
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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)
Forestry Pests, Health and Diseases | Forestry Sciences | Horticultural Crop Improvement (Selection and Breeding) | Conservation and Biodiversity |
ANZSRC Socio-Economic Objective (SEO)
Essential Oil Crops (e.g. Tea Tree, Eucalyptus, Lavender, Peppermint, Boronia, Sandalwood) | Forest and Woodlands Flora, Fauna and Biodiversity
Related Links
Publications
The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae
Publisher: Oxford University Press (OUP)
Date: 11-2021
DOI: 10.1038/S41438-021-00662-4
Abstract: The Rosaceae family has striking phenotypic ersity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a ‘rosetta stone’ for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement ( x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.
Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
Publisher: Public Library of Science (PLoS)
Date: 21-02-2012
Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments
Publisher: Oxford University Press (OUP)
Date: 12-2015
Abstract: The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated in iduals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (& .85) for all traits, and genotype-site interaction accounted for & % of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families.
Evolution and function of red pigmentation in land plants
Publisher: Oxford University Press (OUP)
Date: 07-09-2022
DOI: 10.1093/AOB/MCAC109
Abstract: Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments. In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues theories on the functions of stress-induced pigmentation the evolution of the biosynthetic pathways and structure–function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants. The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.
A genomics approach to understanding the role of auxin in apple (Malus x domestica)fruit size control
Publisher: Springer Science and Business Media LLC
Date: 13-01-2012
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts
Publisher: Cold Spring Harbor Laboratory
Date: 02-08-2023
DOI: 10.1101/2023.07.31.551392
Abstract: Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic ersity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as in idual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Publisher: Cold Spring Harbor Laboratory
Date: 20-03-2020
DOI: 10.1101/2020.03.18.996108
Abstract: Austropuccinia psidii , originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. The overall gene content is highly conserved, when compared to other closely related Pucciniales, yet the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.
Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection
Publisher: Springer Science and Business Media LLC
Date: 21-01-2010
A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition
Publisher: Wiley
Date: 04-08-2021
Abstract: Bilberry ( Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries ( Vaccinium spp.) and cranberry ( V . macrocarpon ). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi‐C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced s les may have been from two in iduals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker‐trait association between these two species, as the loci involved in key characters are orthologous.
The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)
Publisher: Public Library of Science (PLoS)
Date: 03-04-2014
A whole genome assembly of Leptospermum scoparium (Myrtaceae) for mānuka research
Publisher: Informa UK Limited
Date: 02-10-2019
Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data
Publisher: Springer Science and Business Media LLC
Date: 06-04-2020
Stress, senescence, and specialized metabolites in bryophytes
Publisher: Oxford University Press (OUP)
Date: 08-03-2022
DOI: 10.1093/JXB/ERAC085
Abstract: Life on land exposes plants to varied abiotic and biotic environmental stresses. These environmental drivers contributed to a large expansion of metabolic capabilities during land plant evolution and species ersification. In this review we summarize knowledge on how the specialized metabolite pathways of bryophytes may contribute to stress tolerance capabilities. Bryophytes are the non-tracheophyte land plant group (comprising the hornworts, liverworts, and mosses) and rapidly ersified following the colonization of land. Mosses and liverworts have as wide a distribution as flowering plants with regard to available environments, able to grow in polar regions through to hot desert landscapes. Yet in contrast to flowering plants, for which the biosynthetic pathways, transcriptional regulation, and compound function of stress tolerance-related metabolite pathways have been extensively characterized, it is only recently that similar data have become available for bryophytes. The bryophyte data are compared with those available for angiosperms, including examining how the differing plant forms of bryophytes and angiosperms may influence specialized metabolite ersity and function. The involvement of stress-induced specialized metabolites in senescence and nutrient response pathways is also discussed.
High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex
Publisher: Wiley
Date: 21-04-2011
DOI: 10.1111/J.1365-3040.2011.02316.X
Abstract: The biosynthesis of anthocyanin in many plants is affected by environmental conditions. In apple (Malus × domestica Borkh.), concentrations of fruit anthocyanins are lower under hot climatic conditions. We examined the anthocyanin accumulation in the peel of maturing 'Mondial Gala' and 'Royal Gala' apples, grown in both temperate and hot climates, and using artificial heating of on-tree fruit. Heat caused a dramatic reduction of both peel anthocyanin concentration and transcripts of the genes of the anthocyanin biosynthetic pathway. Heating fruit rapidly reduced expression of the R2R3 MYB transcription factor (MYB10) responsible for coordinative regulation for red skin colour, as well as expression of other genes in the transcriptional activation complex. A single night of low temperatures is sufficient to elicit a large increase in transcription of MYB10 and consequently the biosynthetic pathway. Candidate genes that can repress anthocyanin biosynthesis did not appear to be responsible for reductions in anthocyanin content. We propose that temperature-induced regulation of anthocyanin biosynthesis is primarily caused by altered transcript levels of the activating anthocyanin regulatory complex.
Related Organisations
The New Zealand Institute For Plant & Food Research Limited
Location: New Zealand
New Zealand Institute For Plant And Food Research Ltd
Location: New Zealand
Related Funding Activities
Linkage Projects - Grant ID: LP190100093
Start Date: 09-2020
End Date: 12-2023
Amount: $390,000.00
Funder: Australian Research Council
View Funded Activity