Identification of powdery mildew resistance QTL in strawberry (Fragaria × ananassa)

Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry (Fragaria × ananassa)

Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue-specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

Study of a genetic collection of strawberry (Fragaria L.) for resistance to powdery mildew

Powdery mildew (Sphaerotheca macularis Mag. (syn. Podosphaera aphanis Wallr.)) is a dangerous disease of strawberry (Fragaria L.). The resistance of strawberry to powdery mildew is controlled polygenically. Several genetic loci with a large contribution to disease resistance have been identified in various strawberry varieties. Diagnostic DNA markers have been developed for QTL 08 To-f. They showed a high level of reliable gene detection in mapping populations. The purpose of this study was assessment of a strawberry genetic collection for resistance to powdery mildew and identification of promising strawberry forms for breeding for resistance to S. macularis. The objects of the study were wild species of the genus Fragaria L., varieties and selected seedlings of strawberry (Fragaria × ananassa Duch.) created in the I.V. Michurin Federal Scientific Center, and strawberry varieties introduced from various ecological and geographical regions. To identify QTL 08 To-f, DNA markers IB535110 and IB533828 were used. Locus 08 To-f was detected in 23.2 % of the analyzed strawberry genotypes, including wild species F. moschata and F. orientalis, strawberry varieties of Russian breeding (Bylinnaya and Sudarushka) and foreign breeding (Florence, Korona, Malwina, Ostara, Polka and Red Gauntlet). The correlation between the presence of markers IB535110 and IB533828 and phenotypic resistance (powdery mildew effect on strawberry plants is absent) was 0.649. The determination coefficient (R2 ) showing the contribution of the studied locus to the manifestation of the trait was 0.421, that is, in 42.1 % of cases resistance was explained by the presence of QTL 08 To-f, and in 57.9 % of cases, by other genetic factors. All strawberry genotypes with locus 08 To-f were characterized by high field resistance to S. macularis in the conditions of Michurinsk, Tambov region. Thus, locus 08 To-f is promising for conferring resistance on local powdery mildew races, and markers IB535110 and IB533828 can be used in marker-assisted breeding programs to create powdery mildewresistant strawberry genotypes.

Construction of a strawberry breeding core collection to capture and exploit genetic variation

BACKGROUND

Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects.

RESULTS

In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the 'accession to nearest entry' criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program.

CONCLUSIONS

This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.

Genetic analysis and QTL mapping for silique density in rapeseed (Brassica napus L.)

KEY MESSAGE

Genetic models, QTLs and candidate gene for silique density on main inflorescence of rapeseed were identified. Silique density is one of the critical factors to determine seed yield and plant architecture in rapeseed (Brassica napus L.); however, the genetic control of this trait is largely unknown. In this study, the genetic model for silique density on main inflorescence (SDMI) of rapeseed was estimated according to the phenotypic data of P₁ (an inbreed line with high SDMI), P₂ (an inbreed line with low SDMI), F₁, F₂, BC₁P₁ and BC₁P₂ populations, revealing that SDMI is probably controlled by multi-minor genes with or without major gene. The QTLs for SDMI and its component characters including silique number on main inflorescence (SNMI) and main inflorescence length (MIL) were consequently mapped from a DH population derived from P₁ and P₂ by using a genetic linkage map constructed by restriction site-associated DNA sequencing (RAD seq) technology. A total of eight, 14 and three QTLs were identified for SDMI, SNMI and MIL under three environments, respectively, with an overlap among SDMI and SNMI in 55.7-75.4 cm on linkage group C06 which corresponding to 11.6-27.3 Mb on chromosome C06. Genomic resequencing was further conducted between a high- and a low-SDMI pool constructed from the DH population, and QTL-seq analysis identified a 0.15 Mb interval (25.98-26.13 Mb) from the C06-QTL region aforementioned. Transcriptome sequencing and qRT-PCR identified one possible candidate gene (BnARGOS) from the 0.15 Mb interval. This study will provide novel insights into the genetic basis of SD in rapeseed.

A Genomic Resource for the Strawberry Powdery Mildew Pathogen Podosphaera aphanis

Powdery mildew is one of the most economically destructive diseases in protected strawberry production. Here we present the first genome assembly for Podosphaera aphanis, the causal agent of powdery mildew on strawberry. This obligate-biotrophic fungal pathogen was sampled from a naturally occurring outbreak on Fragaria × ananassa 'Malling Centenary' plants grown under cover in the United Kingdom. Assembled reads resolved a 55.6 Mb genome, composed of 12,357 contigs whose annotation led to prediction of 17,239 genes encoding 17,328 proteins. The genome is highly-complete, with 97.5% of conserved single-copy Ascomycete genes shown to be present. This annotated P. aphanis genome provides a molecular resource for further investigation into host-pathogen interactions in the strawberry powdery mildew pathosystem.

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

Real-Time Collection of Conidia Released from Living Single Colonies of Podosphaera aphanis on Strawberry Leaves under Natural Conditions with Electrostatic Techniques

Powdery mildew fungi produce progeny conidia on conidiophores, and promote the spread of powdery mildew diseases by dispersal of the conidia from conidiophores in the natural environment. To gain insights and devise strategies for preventing the spread of powdery mildew infection, it is important to clarify the ecological mechanism of conidial dispersal from conidiophores. In this study, all of the progeny conidia released from single colonies of strawberry powdery mildew fungus (Podosphaera aphanis (Wallroth) U. Braun and S. Takamatsu var. aphanis KSP-7N) on true leaves of living strawberry plants (Fragaria × ananassa Duchesne ex Rozier cv. Sagahonoka) were consecutively collected over the lifetime of the colony with an electrostatic rotational spore collector (insulator drum) under greenhouse conditions, and counted under a high-fidelity digital microscope. The insulator drum consisted of a round plastic container, copper film, thin and transparent collector film, electrostatic voltage generator, and timer mechanism. When negative charge was supplied from the voltage generator to the copper film, the collector film created an attractive force to trap conidia. The electrostatically activated collector film successfully attracted progeny conidia released from the colony. Experiment was carried out at just one colony on one leaf for each month (in February, May, July, October, November, and December in 2021), respectively. Each collector film was exchanged for a new collector film at 24 h intervals until KSP-7N ceased to release progeny conidia from single colonies. Collection experiments were carried out to estimate the total number of conidia released from a single KSP-7N colony over a 35-45-day period after inoculation. During the fungal lifetime, KSP-7N released an average of 6.7 × 10⁴ conidia from each of the single colonies at approximately 816 h. In addition, conidial release from KSP-7N colonies was largely affected by the light intensity and day length throughout a year; the number of conidia released from single KSP-7N colonies in night-time was clearly smaller than that in daytime, and the time of conidial release from single KSP-7N colonies was shorter by approximately 2 to 4 h in autumn and winter than in spring and summer. The ecological characteristics related to conidial releases from KSP-7N colonies will be helpful information for us to successfully suppress the spread of strawberry powdery mildews onto host plants under greenhouse conditions.

Combining canopy reflectance spectrometry and genome-wide prediction to increase response to selection for powdery mildew resistance in cultivated strawberry

High-throughput phenotyping is an emerging approach in plant science, but thus far only a few applications have been made in horticultural crop breeding. Remote sensing of leaf or canopy spectral reflectance can help breeders rapidly measure traits, increase selection accuracy, and thereby improve response to selection. In the present study, we evaluated the integration of spectral analysis of canopy reflectance and genomic information for the prediction of strawberry (Fragaria × ananassa) powdery mildew disease. Two multi-parental breeding populations of strawberry comprising a total of 340 and 464 pedigree-connected seedlings were evaluated in two separate seasons. A single-trait Bayesian prediction method using 1001 spectral wavebands in the ultraviolet-visible-near infrared region (350-1350 nm wavelength) combined with 8552 single nucleotide polymorphism markers showed up to 2-fold increase in predictive ability over models using markers alone. The integration of high-throughput phenotyping was further validated independently across years/trials with improved response to selection of up to 90%. We also conducted Bayesian multi-trait analysis using the estimated vegetative indices as secondary traits. Three vegetative indices (Datt3, REP_Li, and Vogelmann2) had high genetic correlations (rA) with powdery mildew visual ratings with average rA values of 0.76, 0.71, and 0.71, respectively. Increasing training population sizes by incorporating individuals with only vegetative index information yielded substantial increases in predictive ability. These results strongly indicate the use of vegetative indices as secondary traits for indirect selection. Overall, combining spectrometry and genome-wide prediction improved selection accuracy and response to selection for powdery mildew resistance, demonstrating the power of an integrated phenomics-genomics approach in strawberry breeding.

Inheritance of esters and other volatile compounds responsible for the fruity aroma in strawberry

Cultivated strawberry, Fragaria  ×  ananassa, has a complex aroma due to the presence of more than 350 volatile organic compounds (VOCs). However, a mixture of only 19 compounds, called Key Volatile Compounds (KVC), can impart the main strawberry aroma. The octoploid nature of the cultivated strawberry species (2n = 8x = 56) adds complexity to the heritance of the accumulation of the volatiles responsible for aroma. An F1 population cross between two breeding parental lines, FC50 and FD54, was phenotyped for aroma by SPME GCMS during six harvests. A total of 58 compounds were identified: 33 esters, nine terpenes, seven aldehydes, four lactones, two furans, one acid, one alkane and one alcohol, of which 16 were KVCs. A total of 179 QTLs were found, and 85 of these were detected in at least three harvests, of which 50 QTLs were considered major (LOD > 4.0) and detected in five or six analyzed harvests. Several clusters of ester QTLs associated with fruity aroma were discovered, such as QTLs for esters that share hexanoate group that were mapped in LG4A (Hexanoate_4A), those that share acetate and octyl groups in LG6A (Acetate_6A and Octyl_6A) or those with the same methyl group in LG7B (Methyl_7B). Different terpene QTLs associated with floral aroma appear grouped in a cluster in LG3C (Terpene_3C). Some of these clusters of QTLs were validated in a second F2 population, a cross of "Camarosa" and "Dover," that was also phenotyped for three years. Selected SNPs from floral and fruity aroma QTLs were tested in a third population, which will most likely be useful for marker-assisted breeding (MAB).

Shape, firmness and fruit quality QTLs shared in two non-related strawberry populations

The cultivated strawberry (Fragaria x ananassa) is an octoploid species (2n = 8x = 56), appreciated widely for its fruit. There have been very few studies on fruit quality traits, which are known to be mostly polygenic and environmentally dependent. To identify higher genetic variability, two non-related populations were genotyped: an F1 population cross between 'FC50' and 'FD54' and an F2 population cross between 'Camarosa' and 'Dover', hybridizing both with IStraw35k and IStraw90k SNP arrays, respectively. The F1 genetic map was constructed with 14595 SNPs and the F2 map with 7977 SNPs. High collinearity was observed when comparing one genetic map with the other and on comparing both with the octoploid genome. To assess fruit variability, both populations were phenotyped for shape, firmness, taste and other fruit traits over the 2016-2019 period. With QTL analyses, 33 stable QTLs were mapped in the 'FC50xFD54' population, and three hotspot regions were found for shape traits in LG3A, LG4D and LG6D. In the '21AF' population, only eight stable QTLs were detected. Despite that, two major and stable QTLs were mapped in the same interval of confidence for both populations. A shared fruit shape ratio QTL which explained around 25 % of trait variance was mapped in LG3A, and a shared firmness QTL explaining 26.9 % of trait variance in LG7C. For the first time, two QTLs were discovered in LG3A and LG4A for a phenotype neck without achenes. When analysing two different mapping populations, in addition to finding specific QTL regions for the studied traits, a narrowing down of the interval of confidence for the shared QTLs is achieved. As a result of this study, a new set of SNPs for fruit firmness and shape is now available for use in MAS in strawberry breeding programs.

Genomic Informed Breeding Strategies for 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 reported extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and quantitative trait nucleotide (QTN) identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A negative relationship (r = -0.21) between total soluble sugar content and class one yield was identified, indicating a trade-off between these two essential traits. This result highlighted 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 of quantitative trait nucleotide was associated with perceived acidity and pH whereas multiple loci were associated with firmness. Therefore, we recommended the implementation of both marker assisted selection (MAS) and genomic prediction to capture the observed variation respectively. Furthermore, we identified a large effect locus associated with a 10% increase in the number of class one fruit and a further 10 QTN which, when combined, are associated with a 27% increase in the number of marketable strawberries. Ultimately, our results suggested that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruits produced per plant. Not only were strawberry number metrics less influenced by environmental fluctuations, but they had a larger additive genetic component when compared with mass traits. As such, selecting using "number" traits should lead to faster genetic gain.

Defining strawberry shape uniformity using 3D imaging and genetic mapping

Strawberry shape 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 shape 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 potential candidate for marker-assisted breeding, while the potential to implement genomic selection is explored. 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 shape uniformity using 3D imaging tools has allowed precision phenotyping, which has improved the accuracy of trait quantification and unlocked the ability to accurately select for uniform berries.

Genetic and phenotypic associations between root architecture, arbuscular mycorrhizal fungi colonisation and low phosphate tolerance in strawberry (Fragaria × ananassa)

BACKGROUND

Phosphate is an essential plant macronutrient required to achieve maximum crop yield. Roots are able to uptake soil phosphate from the immediate root area, thus creating a nutrient depletion zone. Many plants are able to exploit phosphate from beyond this root nutrient depletion zone through symbiotic association with Arbuscular Mycorrhizal Fungi (AMF). Here we characterise the relationship between root architecture, AMF association and low phosphate tolerance in strawberries. The contrasting root architecture in the parental strawberry cultivars 'Redgauntlet' and 'Hapil' was studied through a mapping population of 168 progeny. Low phosphate tolerance and AMF association was quantified for each genotype to allow assessment of the phenotypic and genotypic relationships between traits.

RESULTS

A "phosphate scavenging" root phenotype where individuals exhibit a high proportion of surface lateral roots was associated with a reduction in root system size across genotypes. A genetic correlation between "root system size" traits was observed with a network of pleiotropic QTL found to represent five "root system size" traits. By contrast, average root diameter and the distribution of roots appeared to be under two discrete methods of genetic control. A total of 18 QTL were associated with plant traits, 4 of which were associated with solidity that explained 46% of the observed variation. Investigations into the relationship between AMF association and root architecture found that a higher root density was associated with greater AMF colonisation across genotypes. However, no phenotypic correlation or genotypic association was found between low phosphate tolerance and the propensity for AMF association, nor root architectural traits when plants are grown under optimal nutrient conditions.

CONCLUSIONS

Understanding the genetic relationships underpinning phosphate capture can inform the breeding of strawberry varieties with better nutrient use efficiency. Solid root systems were associated with greater AMF colonisation. However, low P-tolerance was not phenotypically or genotypically associated with root architecture traits in strawberry plants. Furthermore, a trade-off was observed between root system size and root architecture type, highlighting the energetic costs associated with a "phosphate scavenging" root architecture.

Salicylic acid-primed defence response in octoploid strawberry 'Benihoppe' leaves induces resistance against Podosphaera aphanis through enhanced accumulation of proanthocyanidins and upregulation of pathogenesis-related genes

BACKGROUND

Podosphaera aphanis, a predominately biotrophic fungal pathogen, causes significant yield losses of strawberry. China is the largest strawberry producer in the world, and selecting for powdery mildew-resistant cultivars is desirable. However, the resistance mechanism against P. aphanis in the octoploid strawberry remains unclear.

RESULTS

To understand possible mechanisms of disease resistance, we inoculated strawberry leaves with P. aphanis, and examined the expression profiles of candidate genes and the biochemical phenotypes in strawberry leaves of two groups. The unigenes obtained from ddH₂O- and SA-pretreated leaves resulted in a total of 48,020 and 45,896 genes, respectively. KEGG enrichment showed that phenylpropanoid biosynthesis and plant hormone signal transduction pathways were enriched to a noticeable extent. DEG analysis showed that key TFs genes associated with the SA signaling pathway could play important role in the strawberry-P. aphanis interaction. In particular, FaWRKY70, FaJAZ1 and FaMYC2-like, involved in regulating the antagonistic effect of SA and JA signaling pathway, leading to increased expression of SA-responsive genes (in particular PR1, PR2, PR3, and PR5) compared to a decline in expression of JA-responsive genes (FaJAR1, FaAOS, and FaLOX2). Furthermore, SA pretreatment induced accumulation of PAs by activating the MBW complex and inhibit powdery mildew growth.

CONCLUSIONS

This study describes the role of the proanthocyanidins (PAs), pathogenesis-related (PR) genes, SA, and transcription factors in regulatory model against P. aphanis, which coincided with an early activation of defense, leading to the accumulation of PAs and the PR proteins.

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Identifying Verticillium dahliae Resistance in Strawberry Through Disease Screening of Multiple Populations and Image Based Phenotyping

Verticillium 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 multiple 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." A large-scale low-cost phenotyping platform was developed utilizing 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. A 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 F1 mapping population. Markers identified in 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.

Quantitative trait loci controlling Phytophthora cactorum resistance in the cultivated octoploid strawberry (Fragaria × ananassa)

The cultivated strawberry, Fragaria × ananassa  (Fragaria spp.) is the most economically important global soft fruit. Phytophthora cactorum, a water-borne oomycete causes economic losses in strawberry production globally. A bi-parental cross of octoploid cultivated strawberry segregating for resistance to P. cactorum, the causative agent of crown rot disease, was screened using artificial inoculation. Multiple putative resistance quantitative trait loci (QTL) were identified and mapped. Three major effect QTL (FaRPc6C, FaRPc6D and FaRPc7D) explained 37% of the variation observed. There were no epistatic interactions detected between the three major QTLs. Testing a subset of the mapping population progeny against a range of P. cactorum isolates revealed no significant interaction (p = 0.0593). However, some lines showed higher susceptibility than predicted, indicating that additional undetected factors may affect the expression of some quantitative resistance loci. Using historic crown rot disease score data from strawberry accessions, a preliminary genome-wide association study (GWAS) of 114 individuals revealed an additional locus associated with resistance to P. cactorum. Mining of the Fragaria vesca Hawaii 4 v1.1 genome revealed candidate resistance genes in the QTL regions.

Identification of QTLs for powdery mildew (Podosphaera aphanis; syn. Sphaerotheca macularis f. sp. fragariae) susceptibility in cultivated strawberry (Fragaria ×ananassa)

Strawberry powdery mildew (Podosphaera aphanis Wallr.) is a pathogen which infects the leaves, fruit, stolon and flowers of the cultivated strawberry (Fragaria ×ananassa), causing major yield losses, primarily through unmarketable fruit. The primary commercial control of the disease is the application of fungicidal sprays. However, as the use of key active ingredients of commercial fungicides is becoming increasingly restricted, interest in developing novel strawberry cultivars exhibiting resistance to the pathogen is growing rapidly. In this study, a mapping population derived from a cross between two commercial strawberry cultivars ('Sonata' and 'Babette') was genotyped with single nucleotide polymorphism (SNP) markers from the Axiom iStraw90k genotyping array and phenotyped for powdery mildew susceptibility in both glasshouse and field environments. Three distinct, significant QTLs for powdery mildew resistance were identified across the two experiments. Through comparison with previous studies and scrutiny of the F. vesca genome sequence, candidate genes underlying the genetic control of this trait were identified.