Browsing by Author "Wright K"

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    Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes
    (BioMed Central Ltd, 2023-05-05) Angelin-Bonnet O; Thomson S; Vignes M; Biggs PJ; Monaghan K; Bloomer R; Wright K; Baldwin S
    BACKGROUND: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS: When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION: This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.
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    Organisational response to the 2007 Ruapehu Crater Lake breakout lahar in New Zealand: Use of communication in creating an effective response
    (Springer International Publishing, 2016-01-05) Becker J; Leonard GJ; Potter SH; Coomer MA; Paton D; Wright K; Johnston DM; Fearnley, C; Bird, D; Jolly, GE; Haynes, K
    When Mt. Ruapehu erupted in 1995-1996 in New Zealand, a tephra barrier was created alongside Crater Lake on the top of Mt. Ruapehu. This barrier acted as a dam, with Crater Lake rising behind it over time. In 2007 the lake breached the dam and a lahar occurred down the Whangaehu Valley and across the volcano’s broad alluvial ring-plain. Given the lahar history from Ruapehu, the risk from the 2007 event was identified beforehand and steps taken to reduce the risks to life and infrastructure. An early warning system was set up to notify when the dam had broken and the lahar had occurred. Physical works to mitigate the risk were put in place. A planning group was also formed and emergency management plans were put in place to respond to the risk. To assess the effectiveness of planning for and responding to the lahar, semi-structured interviews were undertaken with personnel from key organisations both before and after the lahar event. This chapter discusses the findings from the interviews in the context of communications, and highlights how good communications contributed to an effective emergency management response. As the potential for a lahar was identifiable, approximately 10 years of lead-up time was available to install warning system hardware, implement physical mitigation measures, create emergency management plans, and practice exercises for the lahar. The planning and exercising developed effective internal communications, engendered relationships, and moved individuals towards a shared mental model of how a respond to the event. Consequently, the response played out largely as planned with only minor communication issues occurring on the day of the lahar. The minor communication issues were due to strong personal connections leading to at least one case of the plan being bypassed. Communication levels during the lahar event itself were also different from that experienced in exercises, and in some instances communications were seen to increase almost three-fold. This increase in level of communication, led to some difficulty in getting through to the main Incident Control Point. A final thought regarding public communications prior to the event was that more effort could have been given to developing and integrating public information about the lahar, to allow for ease of understanding about the event and integration of information across agencies.