Browsing by Author "Williams NM"

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    Assessing the genetic variation of tolerance to red needle cast in a Pinus radiata breeding population
    (Springer-Verlag GmbH Germany, part of Springer Nature, 2018-06-27) Graham NJ; Suontama M; Pleasants T; Li Y; Bader MKF; Klápště J; Dungey HS; Williams NM
    Breeding for disease resistance or tolerance is a viable option for disease management programmes and is important for the continued success and resilience of planted forests. Red needle cast (RNC) is a disease that affects radiata pine (Pinus radiata) and is caused by Phytophthora pluvialis. Knowledge is still very limited regarding the potential for genetic tolerance to this pathogen. The application of controlled screening techniques is clearly required. Using a detached needle assay, we screened 392 clonally replicated individuals (clones) from an elite P. radiata population for quantitative tolerance to RNC. Data was highly skewed and required logarithmic data transformation and Poisson distributions for the estimation of best linear unbiased predictions. These estimates revealed a broad range in susceptibility/tolerance to RNC, and enabled the identification of clones that were clearly susceptible and clones that were clearly tolerant. There was a high correlation between the number and length of lesions that developed in response to inoculation with P. pluvialis. Broad-sense heritability estimates were low to moderate, indicating that there is potential for improving tolerance through breeding. These results provide evidence that breeding for tolerance to P. pluvialis is possible, although continued work into understanding and minimising causes for variance are required.
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    Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families
    (Frontiers Media S.A., 2022-11-02) Cox MP; Guo Y; Winter DJ; Sen D; Cauldron NC; Shiller J; Bradley EL; Ganley AR; Gerth ML; Lacey RF; McDougal RL; Panda P; Williams NM; Grunwald NJ; Mesarich CH; Bradshaw RE; Hane J
    Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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    Why a strategic shift in action is needed to recognise and empower Indigenous plant pathology knowledge and research
    (Springer Nature on behalf of the Australasian Plant Pathology Society Inc, 2024-05-01) Ehau-Taumaunu H; Williams NM; Marsh A; Waipara NW; Higgins CM; Geering ADW; Mesarich CH; Rigano LA; Summerell BA; Johnson GI; Williamson P; MacDiarmid RM
    Plant pathology researchers play a pivotal role in thought leadership and its translation to action regarding the recognition and demonstration of the value of Indigenous knowledge and science. For many scientists, navigating the space of Indigenous rights and perspectives is challenging. In pursuit of a cultural shift in research and development within the field of plant pathology, the 2019–2021 Management Committee of the Australasian Plant Pathology Society (APPS) undertook a review and modernization of the Society’s Constitution. The aim was to ensure its alignment with principles that foster inclusivity of Indigenous peoples in the development and implementation of relevant research projects impacting their communities. Additionally, a dynamic repository of guidelines and resources was compiled. These resources are designed to assist plant pathologists, while respecting and not superseding the guidance provided by local Indigenous researchers, practitioners, and advisors. The collective efforts of plant pathologists hold immense potential in championing Indigenous Peoples and their rights, steering the field toward a more inclusive and equitable future. This paper builds upon the thesis presented in the APPS Presidential Address at the Biennial APPS Conference in 2021, held virtually in lutruwita (Tasmania) on the unceded lands of the Palawa people. It underscores the potential impact when plant pathologists unite in advocating for Indigenous Peoples and their rightful place within the field.