Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa)

Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry

Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × $\times$ ananassa), has caused economic losses for nearly a century. This disease is caused by the soil-borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW-resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n = 564 $n = 564$ ) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n = 386 $n = 386$ ), genomic prediction accuracies of 0.47-0.48 were achieved and were predicted to explain 70%-75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.

New insights into defense responses against Verticillium dahliae infection revealed by a quantitative proteomic analysis in Arabidopsis thaliana

Verticillium wilt is a highly destructive fungal disease that attacks a broad range of plants, including many major crops. However, the mechanism underlying plant immunity toward Verticillium dahliae is very complex and requires further study. By combining bioinformatics analysis and experimental validation, we investigated plant defence responses against V. dahliae infection in the model plant Arabidopsis thaliana L. A total of 301 increased and 214 decreased differentially abundant proteins (DAPs) between mock and infected wild type (WT) plants were acquired and bioinformatics analyses were then conducted and compared (increased vs decreased) in detail. In addition to the currently known mechanisms, several new clues about plant immunity against V. dahliae infection were found in this study: (1) exosome formation was dramatically induced by V. dahliae attack; (2) tryptophan-derived camalexin and cyanogenic biosynthesis were durably promoted in response to infection; and (3) various newly identified components were activated for hub immunity responses. These new clues provide valuable information that extends the current knowledge about the molecular basis of plant immunity against V. dahliae infection.

On-field phenotypic evaluation of sunflower populations for broad-spectrum resistance to Verticillium leaf mottle and wilt

Sunflower Verticillium Wilt and Leaf Mottle (SVW), caused by Verticillium dahliae (Kleb.; Vd), is a soil-borne disease affecting sunflower worldwide. A single dominant locus, known as V1, was formerly effective in controlling North-American Vd races, whereas races from Argentina, Europe and an emerging race from USA overcome its resistance. This emphasizes the need for identifying broad-spectrum genetic resistance (BSR) sources. Here we characterize two sunflower mapping populations (MPs) for SVW resistance: a biparental MP and the association MP from the National Institute of Agricultural Technology (INTA), under field growing conditions. Nine field-trials (FTs) were conducted in highly infested fields in the most SVW-affected region of Argentina. Several disease descriptors (DDs), including incidence and severity, were scored across four phenological stages. Generalized linear models were fitted according to the nature of each variable, adjusting mean phenotypes for inbred lines across and within FTs. Comparison of these responses allowed the identification of novel BSR sources. Furthermore, we present the first report of SVW resistance heritability, with estimates ranging from 35 to 45% for DDs related to disease incidence and severity, respectively. This study constitutes the largest SVW resistance characterization reported to date in sunflower, identifying valuable genetic resources for BSR-breeding to cope with a pathogen of increasing importance worldwide.

Genetics of Partial Resistance Against Verticillium dahliae Race 2 in Wild and Cultivated Lettuce

Lettuce (Lactuca sativa) is one of the most economically important vegetables in the United States, with approximately 50% of the domestic production concentrated in the Salinas Valley of California. Verticillium wilt, caused by races 1 and 2 of the fungal pathogen Verticillium dahliae, poses a major threat to lettuce production in this area. Although resistance governed by a single dominant gene against race 1 has previously been identified and is currently being incorporated into commercial cultivars, identification of resistance against race 2 has been challenging and no lines with complete resistance have been identified. In this study, we screened germplasm for resistance and investigated the genetics of partial resistance against race 2 using three mapping populations derived from crosses involving L. sativa × L. sativa and L. serriola × L. sativa. The inheritance of resistance in Lactuca species against race 2 is complex but a common quantitative trait locus (QTL) on linkage group 6, designated qVERT6.1 (quantitative Verticillium dahliae resistance on LG 6, first QTL), was detected in multiple populations. Additional race 2 resistance QTLs located in several linkage groups were detected in individual populations and environments. Because resistance in lettuce against race 2 is polygenic with a large genotype by environment interaction, breeding programs to incorporate these resistance genes should be aware of this complexity as they implement strategies to control race 2.

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.

Blocking intruders: inducible physico-chemical barriers against plant vascular wilt pathogens

Xylem vascular wilt pathogens cause devastating diseases in plants. Proliferation of these pathogens in the xylem causes massive disruption of water and mineral transport, resulting in severe wilting and death of the infected plants. Upon reaching the xylem vascular tissue, these pathogens multiply profusely, spreading vertically within the xylem sap, and horizontally between vessels and to the surrounding tissues. Plant resistance to these pathogens is very complex. One of the most effective defense responses in resistant plants is the formation of physico-chemical barriers in the xylem tissue. Vertical spread within the vessel lumen is restricted by structural barriers, namely, tyloses and gels. Horizontal spread to the apoplast and surrounding healthy vessels and tissues is prevented by vascular coating of the colonized vessels with lignin and suberin. Both vertical and horizontal barriers compartmentalize the pathogen at the infection site and contribute to their elimination. Induction of these defenses are tightly coordinated, both temporally and spatially, to avoid detrimental consequences such as cavitation and embolism. We discuss current knowledge on mechanisms underlying plant-inducible structural barriers against major xylem-colonizing pathogens. This knowledge may be applied to engineer metabolic pathways of vascular coating compounds in specific cells, to produce plants resistant towards xylem colonizers.

Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry

Verticillium wilt, a soil-borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a persistent challenge, in part because the genetics of resistance is complex. The heritability of resistance and genetic gains in breeding for resistance to this pathogen have not been well documented. To elucidate the genetics, assess long-term genetic gains, and estimate the accuracy of genomic selection for resistance to Verticillium wilt, we analyzed a genetically diverse population of elite and exotic germplasm accessions (n = 984), including 245 cultivars developed since 1854. We observed a full range of phenotypes, from highly susceptible to highly resistant: < 3% were classified as highly resistant, whereas > 50% were classified as moderately to highly susceptible. Broad-sense heritability estimates ranged from 0.70-0.76, whereas narrow-sense genomic heritability estimates ranged from 0.33-0.45. We found that genetic gains in breeding for resistance to Verticillium wilt have been negative over the last 165 years (mean resistance has decreased over time). We identified several highly resistant accessions that might harbor favorable alleles that are either rare or non-existent in modern populations. We did not observe the segregation of large-effect loci. The accuracy of genomic predictions ranged from 0.38-0.53 among years and whole-genome regression methods. We show that genomic selection has promise for increasing genetic gains and accelerating the development of resistant cultivars in strawberry by shortening selection cycles and enabling selection in early developmental stages without phenotyping.

Hop Polyphenols in Relation to Verticillium Wilt Resistance and Their Antifungal Activity

(1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne fungi Verticillium nonalfalfae and Verticillium dahliae. As suggested by quantitative trait locus (QTL) mapping and RNA-Seq analyses, the underlying molecular mechanisms of resistance in hop are complex, consisting of preformed and induced defense responses, including the synthesis of various phenolic compounds. (2) Methods: We determined the total polyphenolic content at two phenological stages in roots and stems of 14 hop varieties differing in VW resistance, examined the changes in the total polyphenols of VW resistant variety Wye Target (WT) and susceptible Celeia (CE) on infection with V. nonalfalfae, and assessed the antifungal activity of six commercial phenolic compounds and total polyphenolic extracts from roots and stems of VW resistant WT and susceptible CE on the growth of two different V. nonalfalfae hop pathotypes. (3) Results: Generally, total polyphenols were higher in roots than stems and increased with maturation of the hop. Before flowering, the majority of VW resistant varieties had a significantly higher content of total polyphenols in stems than susceptible varieties. At the symptomatic stage of VW disease, total polyphenols decreased in VW resistant WT and susceptible CE plants in both roots and stems. The antifungal activity of total polyphenolic extracts against V. nonalfalfae was higher in hop extracts from stems than those from roots. Among the tested phenolic compounds, only p-coumaric acid and tyrosol markedly restricted fungal growth. (4) Conclusions: Although the correlation between VW resistance and total polyphenols content is not straightforward, higher levels of total polyphenols in the stems of the majority of VW resistant hop varieties at early phenological stages probably contribute to fast and efficient activation of signaling pathways, leading to successful defense against V. nonalfalfae infection.

Strawberries at the Crossroads: Management of Soilborne Diseases in California Without Methyl Bromide

Strawberry production has historically been affected by soilborne diseases such as Verticillium wilt. This disease was a major limiting factor in strawberry production in California in the 1950s and was the main reason that preplant soil fumigation with methyl bromide (MB) was developed in the late 1950s. MB fumigation was so successful that over 90% of the commercial strawberry fruit production in California utilized this technique. However, MB was subsequently linked to ozone depletion, and its use was phased out in 2005. The California strawberry industry was awarded exemption to the full phase-out until 2016, when all MB use in strawberry fruit production was prohibited. MB use continues in strawberry nurseries under an exemption to prevent spread of nematodes and diseases on planting stock. This review examines the impact of the MB phase-out on the California strawberry industry and evaluates the outlook for the industry in the absence of one of the most effective tools for managing soilborne diseases. New soilborne diseases have emerged, and historically important soilborne diseases have reemerged. Registration of new fumigants has been difficult and replacement of MB with a new and effective alternative is unlikely in the foreseeable future. Thus, crop losses due to soilborne diseases are likely to increase. Host plant resistance to soilborne diseases has become a top priority for strawberry breeding programs, and cultivars are increasingly selected for their resistance to soilborne diseases. The intelligent integration of a variety of management tactics is necessary to sustain strawberry production in California.

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.

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.

FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry

Optimal strategies for genetic improvement in crops depend on accurate assessments of the genetic architecture of traits. The overall objective of the present study was to determine the genetic architecture of anthracnose fruit rot (AFR) resistance caused by the fungus Colletotrichum acutatum in the University of Florida strawberry (Fragaria × ananassa) breeding germplasm. In 2016-2017, 33 full-sib families resulting from crosses between parents with varying levels of AFR resistance were tested. In 2017-2018, six full-sib families resulting from putative heterozygous resistant parents and homozygous susceptible parents were tested. Additionally, a validation population consisting of 77 advanced selections and ten cultivars was tested in the second season. Inoculation was performed using a mixture of three local isolates of the C. acutatum species complex. Phenotypes were scored weekly, and genotyping was performed using the IStraw35 Affymetrix Axiom® SNP array. A pedigree-based QTL analysis was performed using FlexQTL™ software. A major resistance locus, which we name FaRCa1, was detected in both seasons with a peak located at 55-56 cM on LG 6B and explaining at least 50% of the phenotypic variation across trials and seasons. The resistant allele exhibited partial dominance in all trials. The FaRCa1 locus is distinct from the previously discovered Rca2 locus, which mapped to LG 7B. While Rca2 is effective against European isolates from pathogenicity group 2, FaRCa1 appears to confer resistance to isolates of pathogenicity group 1.

Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry

Verticillium dahliae infection of strawberry (Fragaria x ananassa) is a major cause of disease-induced wilting in soil-grown strawberries across the world. To understand what components of the pathogen are affecting disease expression, the presence of the known effector VdAve1 was screened in a sample of Verticillium dahliae isolates. Isolates from strawberry were found to contain VdAve1 and were divided into two major clades, based upon their vegetative compatibility groups (VCG); no UK strawberry isolates contained VdAve1. VC clade was strongly related to their virulence levels. VdAve1-containing isolates pathogenic on strawberry were found in both clades, in contrast to some recently published findings. On strawberry, VdAve1-containing isolates had significantly higher virulence during early infection, which diminished in significance as the infection progressed. Transformation of a virulent non-VdAve1 containing isolate, with VdAve1 was found neither to increase nor decrease virulence when inoculated on a susceptible strawberry cultivar. There are therefore virulence factors that are epistatic to VdAve1 and potentially multiple independent routes to high virulence on strawberry in V. dahliae lineages. Genome sequencing a subset of isolates across the two VCGs revealed that isolates were differentiated at the whole genome level and contained multiple changes in putative effector content, indicating that different clonal VCGs may have evolved different strategies for infecting strawberry, leading to different virulence levels in pathogenicity tests. It is therefore important to consider both clonal lineage and effector complement as the adaptive potential of each lineage will differ, even if they contain the same race determining effector.

Transfer of tomato immune receptor Ve1 confers Ave1-dependent Verticillium resistance in tobacco and cotton

Verticillium wilts caused by soilborne fungal species of the Verticillium genus are economically important plant diseases that affect a wide range of host plants and are notoriously difficult to combat. Perception of pathogen(-induced) ligands by plant immune receptors is a key component of plant innate immunity. In tomato, race-specific resistance to Verticillium wilt is governed by the cell surface-localized immune receptor Ve1 through recognition of the effector protein Ave1 that is secreted by race 1 strains of Verticillium spp. It was previously demonstrated that transgenic expression of tomato Ve1 in the model plant Arabidopsis thaliana leads to Verticillium wilt resistance. Here, we investigated whether tomato Ve1 can confer Verticillium resistance when expressed in the crop species tobacco (Nicotiana tabcum) and cotton (Gossypium hirsutum). We show that transgenic tobacco and cotton plants constitutively expressing tomato Ve1 exhibit enhanced resistance against Verticillium wilt in an Ave1-dependent manner. Thus, we demonstrate that the functionality of tomato Ve1 in Verticillium wilt resistance through recognition of the Verticillium effector Ave1 is retained after transfer to tobacco and cotton, implying that the Ve1-mediated immune signalling pathway is evolutionary conserved across these plant species. Moreover, our results suggest that transfer of tomato Ve1 across sexually incompatible plant species can be exploited in breeding programmes to engineer Verticillium wilt resistance.

Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis

Verticillium wilt, caused by soil-borne fungi of the genus Verticillium, is an economically important disease that affects a wide range of host plants. Unfortunately, host resistance against Verticillium wilts is not available for many plant species, and the disease is notoriously difficult to combat. Host-induced gene silencing (HIGS) is an RNA interference (RNAi)-based process in which small RNAs are produced by the host plant to target parasite transcripts. HIGS has emerged as a promising strategy for the improvement of plant resistance against pathogens by silencing genes that are essential for these pathogens. Here, we assessed whether HIGS can be utilized to suppress Verticillium wilt disease by silencing three previously identified virulence genes of V. dahliae (encoding Ave1, Sge1 and NLP1) through the host plants tomato and Arabidopsis. In transient assays, tomato plants were agroinfiltrated with Tobacco rattle virus (TRV) constructs to target V. dahliae transcripts. Subsequent V. dahliae inoculation revealed the suppression of Verticillium wilt disease on treatment with only one of the three TRV constructs. Next, expression of RNAi constructs targeting transcripts of the same three V. dahliae virulence genes was pursued in stable transgenic Arabidopsis thaliana plants. In this host, V. dahliae inoculation revealed reduced Verticillium wilt disease in two of the three targets. Thus, our study suggests that, depending on the target gene chosen, HIGS against V. dahliae is operational in tomato and A. thaliana plants and may be exploited to engineer resistance in Verticillium wilt-susceptible crops.

Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor

Plant-pathogenic microbes secrete effector molecules to establish themselves on their hosts, whereas plants use immune receptors to try and intercept such effectors in order to prevent pathogen colonization. The tomato cell surface-localized receptor Ve1 confers race-specific resistance against race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae which secrete the Ave1 effector. Here, we describe the cloning and characterization of Ve1 homologues from tobacco (Nicotiana glutinosa), potato (Solanum tuberosum), wild eggplant (Solanum torvum) and hop (Humulus lupulus), and demonstrate that particular Ve1 homologues govern resistance against V. dahliae race 1 strains through the recognition of the Ave1 effector. Phylogenetic analysis shows that Ve1 homologues are widely distributed in land plants. Thus, our study suggests an ancient origin of the Ve1 immune receptor in the plant kingdom.