Biology subjects

Cockerton, H. M.

Publications and source records attributed to Cockerton, H. M..

7 recordsLinked to original sources

bioRxiv2026

Dynamic gene gain and loss during the divergence of obligate biotrophic powdery mildew pathogens

Powdery mildew outbreaks can result in devastating crop losses across both horticultural and cereal crops. The obligate biotrophic fungi responsible (Erysiphaceae) depend entirely on living plant hosts for survival, extracting nutrients exclusively from living host tissue. Despite their impact, genomic resources for dicot-infecting powdery mildew fungi remain limited, restricting understanding of differentiation in the effector complements that underpin biotrophy across mildew lineages. To address this, we sequenced and assembled genomes from three independent samples each of Podosphaera leucotricha (apple mildew) and P. aphanis sensu lato (strawberry & raspberry mildew). These novel genomes were analysed alongside 44 publicly-available Erysiphaceae genomes to reveal striking inter-species differences in effectorome complements. P. leucotricha encoded the largest predicted effector complement of any powdery mildew pathogen sequenced to date, with major expansions in RALPH and EKA effector families. By contrast, the closely related P. aphanis carried a comparatively small effector repertoire. Together, these data challenge the prevailing view that effector expansion is restricted to monocot-infecting mildews. We observed that the divergence of powdery mildew genera is associated with the contraction of gene families, consistent with a stepwise loss of genes. This pattern was also reflected in the loss of genes that are typically conserved across ascomycete fungi. Taken together our findings highlight the contrasting impact that biotrophic adaptation has had on pathogen genomes, namely the convergent loss of conserved fungal genes alongside the diversification of pathogen effectoromes in response to host immune landscapes.

plant biology↗

bioRxiv2021

The Genetic Architecture of Strawberry Yield and Fruit Quality Traits

Over the last two centuries breeders have drastically modified the fruit quality of strawberries through artificial selection. However, there remains significant variation in quality across germplasm with scope for further improvements to be made. We report extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and QTL identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A trade-off was observed between two essential traits: sugar content and class one yield. This result highlights an established dilemma for strawberry breeders and a need to uncouple the relationship, particularly under June-bearing, protected production systems comparable to this study. A large effect QTL was associated with perceived acidity and pH whereas multiple loci were associated with firmness, we therefore recommend the implementation of both MAS and genomic prediction to capture the observed variation respectively. Ultimately, our results suggest that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruit produced per plant. Strawberry number metrics were less influenced by environmental fluctuations and had a larger additive genetic component when compared to mass traits. As such, selecting using "number" traits should lead to faster genetic gain. Finally, we identify a large effect locus associated with an increase in class one fruit.

plant biology↗

bioRxiv2021

Fitness cost associated with enhanced EPSPS gene copy number and glyphosate resistance in an Amaranthus tuberculatus population

The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. Following the production of seed families with contrasting levels of glyphosate resistance, we assessed the growth and fitness of seed families in the absence of glyphosate and determined their ability to compete for resources under intra- and interspecific competition. Further investigation revealed a positive correlation between the level of resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus indicating gene amplification as the mechanism of resistance within the population. Resistant common waterhemp plants were found to have a lower competitive response when compared to the susceptible phenotypes. A substitution rate of 2.76 glyphosate resistant plants was required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.

plant biology↗

bioRxiv2020

Defining Strawberry Uniformity using 3D Imaging and Genetic Mapping

Strawberry uniformity is a complex trait, influenced by multiple genetic and environmental components. To complicate matters further, the phenotypic assessment of strawberry uniformity is confounded by the difficulty of quantifying geometric parameters by eye and variation between assessors. An in-depth genetic analysis of strawberry uniformity has not been undertaken to date, due to the lack of accurate and objective data. Nonetheless, uniformity remains one of the most important fruit quality selection criteria for the development of a new variety. In this study, a 3D-imaging approach was developed to characterise berry uniformity. We show that circularity of the maximum circumference had the closest predictive relationship with the manual uniformity score. Combining five or six automated metrics provided the best predictive model, indicating that human assessment of uniformity is highly complex. Furthermore, visual assessment of strawberry fruit quality in a multi-parental QTL mapping population has allowed the identification of genetic components controlling uniformity. A "regular shape" QTL was identified and found to be associated with three uniformity metrics. The QTL was present across a wide array of germplasm, indicating a strong candidate for marker-assisted breeding. A greater understanding of berry uniformity has been achieved through the study of the relative impact of automated metrics on human perceived uniformity. Furthermore, the comprehensive definition of strawberry uniformity using 3D imaging tools has allowed precision phenotyping, which has improved the accuracy of trait quantification. This tool has allowed us to illustrate the use of advanced image analysis towards the breeding of greater uniformity in strawberry.

bioinformatics↗

bioRxiv2019

Genomics, evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes

The Alternaria section alternaria (A. alternata species group) represents a diverse group of saprophytes, human allergens and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear and strawberry pathotypes, providing new tools for pathogen diagnostics.

microbiology↗

bioRxiv2018

Image-based Phenotyping and Disease Screening of Multiple Populations for resistance to Verticillium dahliae in cultivated strawberry Fragaria x ananassa

1.0Verticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in biparental strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar Redgauntlet and subclade II-2 specific resistance in Fenella and Chandler.\n\nA large-scale low-cost phenotyping platform was developed utilising automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores.\n\nA co-dominant resistant QTL; FaRVd3D, present in both Redgauntlet and Hapil cultivars exhibited a major effect of 18.3 % when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the Emily cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the bi-parental cross.\n\nMarkers identified in bi-parental populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from Redgauntlet and FaRVd6D from Chandler were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.

genetics↗

bioRxiv2018

Identification of powdery mildew resistance QTL in Fragaria x ananassa

The obligate biotrophic fungus Podosphaera aphanis is the causative agent of powdery mildew on cultivated strawberry (Fragaria x ananassa). Genotypes from two bi-parental mapping populations Emily x Fenella and Redgauntlet x Hapil were phenotyped for powdery mildew disease severity in a series of field trials. Here we report multiple QTL associated with resistance to powdery mildew, identified in ten phenotyping events conducted across different years and locations. Seven QTL show a level of stable resistance across multiple phenotyping events however many other QTL were represented in a single phenotyping event and therefore must be considered transient. One of the identified QTL was closely linked to an associated resistance gene across the wider germplasm. Furthermore, a preliminary association analysis identified a novel conserved locus for further investigation. Our data suggests that resistance is highly complex and that multiple additive sources of quantitative resistance to powdery mildew exist across strawberry germplasm. Implementation of the reported markers in marker-assisted breeding or genomic selection would lead to improved powdery mildew resistant strawberry cultivars, particularly where the studied parents, progeny and close pedigree material are included in breeding germplasm.\n\nKey MessagePowdery mildew resistance in two strawberry mapping populations is controlled by both stable and transient novel QTL of moderate effect. Some transferability of QTL across wider germplasm was observed.

pathology↗