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Key messageWe demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses. Notably, homologues of Secreted in Xylem (SIX) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed. [ABSTRACT FROM AUTHOR]

Carrot is a major root vegetable crop grown in many parts of the world. In Europe, cavity spot disease continues to have a major impact on marketable yield. The disease is caused by several Pythium spp., with P. violae the main pathogen in the UK and results in small black lesions on mature carrot roots. The lack of reliable inoculation methods for these Pythium pathogens has, for many years, hampered the identification of new effective crop protection products or carrot varieties that are resistant to the disease. In this research, inoculation methods were developed for P. violae using mycelium or oospores, each of which successfully induced typical cavity spot symptoms in both pot‐ and field‐grown carrots as well as consistent root stunting in the former. These methods were also used to successfully identify carrot cultivars with resistance to cavity spot and confirmed the efficacy of the fungicide metalaxyl‐M against the disease. Results therefore demonstrated that the inoculation methods should be reliable for identifying the efficacy of crop protection products, assessing cavity spot resistance and for further studies investigating the biology and epidemiology of the pathogen. [ABSTRACT FROM AUTHOR]

Thermal imaging has been used in the past for remote detection of regions of canopy showing symptoms of stress, including water deficit stress. Stress indices derived from thermal images have been used as an indicator of canopy water status, but these depend on the choice of reference surfaces and environmental conditions and can be confounded by variations in complex canopy structure. Therefore, in this work, instead of using stress indices, information from thermal and visible light imagery was combined along with machine learning techniques to identify regions of canopy showing a response to soil water deficit. Thermal and visible light images of a spinach canopy with different levels of soil moisture were captured. Statistical measurements from these images were extracted and used to classify between canopies growing in well-watered soil or under soil moisture deficit using Support Vector Machines (SVM) and Gaussian Processes Classifier (GPC) and a combination of both the classifiers. The classification results show a high correlation with soil moisture. We demonstrate that regions of a spinach crop responding to soil water deficit can be identified by using machine learning techniques with a high accuracy of 97%. This method could, in principle, be applied to any crop at a range of scales.

Fifteen fathers of children with disabilities living in urban and rural settings in New Zealand were interviewed about their experiences, which included their interactions with teachers and others in the school system. Eight key concerns of the fathers are discussed along with implications for policy and practice. (Author/CR)

Abstract Background There is an increasing recognition that modelling and simulation can assist in the process of designing health care policies, strategies and operations. However, the current use is limited and answers to questions such as what methods to use and when remain somewhat underdeveloped. Aim The aim of this study is to provide a mechanism for decision makers in health services planning and management to compare a broad range of modelling and simulation methods so that they can better select and use them or better commission relevant modelling and simulation work. Methods This paper proposes a modelling and simulation method comparison and selection tool developed from a comprehensive literature review, the research team's extensive expertise and inputs from potential users. Twenty-eight different methods were identified, characterised by their relevance to different application areas, project life cycle stages, types of output and levels of insight, and four input resources required (time, money, knowledge and data). Results The characterisation is presented in matrix forms to allow quick comparison and selection. This paper also highlights significant knowledge gaps in the existing literature when assessing the applicability of particular approaches to health services management, where modelling and simulation skills are scarce let alone money and time. Conclusions A modelling and simulation method comparison and selection tool is developed to assist with the selection of methods appropriate to supporting specific decision making processes. In particular it addresses the issue of which method is most appropriate to which specific health services management problem, what the user might expect to be obtained from the method, and what is required to use the method. In summary, we believe the tool adds value to the scarce existing literature on methods comparison and selection.

Fusarium proliferatum is a globally distributed fungal pathogen that affects a range of crop hosts and is one of the main producers of mycotoxins, such as fumonisins, in foods. Specific PCR primers are commonly used for detection and identification of this pathogen. The aim of this study was to validate previously published F. proliferatum‐specific primers targeting the intergenic spacer (IGS) region and characterize intraspecific variation and homologous recombination events for isolates obtained from diseased garlic bulbs in Spain. Sixty‐nine isolates were morphologically identified as F. proliferatum, and their identity was confirmed by sequencing of the translation elongation factor; however, specific IGS primers did not result in an amplification product for nine of these isolates. Further analysis showed that this was due to polymorphism in the IGS region and six isolates were classified as IGS type I, while the remaining isolates were type II. Sequencing of the complete IGS region revealed numerous sequence polymorphisms amongst F. proliferatum isolates, and regions of recombination. Duplication and deletion events may have occurred via unequal crossing over during mitotic or meiotic recombination. These results suggest that the IGS region may be too variable as a reliable target for F. proliferatum‐specific identification. [ABSTRACT FROM AUTHOR]