Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry

Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pathogen, began surfacing in California, Florida, and elsewhere. This disease has since become one of the most common causes of plant death and yield losses in strawberry. The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses. Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious. The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress. The genetic gains were immediate and dramatic. The frequency of highly resistant individuals increased from 1% in selection cycle 0 to 74% in selection cycle 2. Using GWAS and survival analysis, we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance. An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies, which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.

Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant to Fusarium oxysporum f. sp. fragariae, a devastating soil-borne pathogen of strawberry. Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria [Formula: see text] ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

Genetic Diversity and Potential Inoculum Sources of Fusarium Species Causing Cankers in Bareroot-Propagated Almond Trees in California Nurseries

Previous research determined that Fusarium acuminatum and F. avenaceum are important causal agents of a canker disease in bareroot-propagated fruit and nut trees in California that emerges during cold storage or after transplanting. The disease largely disappeared after 2001, but it reemerged in 2011 in almond trees in at least one nursery. This motivated further study of the etiology and epidemiology of the disease by undertaking studies to determine distribution of the pathogens throughout almond nursery propagation systems and trace possible sources of inoculum. Research initiated in 2013 detected pathogenic Fusarium spp. throughout the almond propagation system, including in healthy trees, in soils, on wheat rotation crops, on equipment, and in the cold-storage facility air. In addition to the two Fusarium spp. implicated previously, F. brachygibbosum and a new Fusarium species, F. californicum, were found to be pathogenic on almond trees. Multilocus sequence typing and somatic compatibility testing confirmed that isolates within a species collected from different materials in the nursery were all highly genetically similar and likely of one clonal lineage. These findings affirm that equipment surfaces, wheat rotation crops, soil, cold-storage facility air, and asymptomatic almond tree materials (i.e., rootstock cuttings, budwood, and scions) can potentially contribute inoculum to increase disease prevalence and severity.

Tolerance of 2-Benzoxazolinone and Interactions with Grass and Pine Hosts in a Population of Fusarium circinatum

Fusarium circinatum, the causal agent of pitch canker in pines and a cryptic endophyte of grasses, was examined for heritable variation in tolerance of the grass defense compound 2-benzoxazolinone (BOA). A diverse population of F. circinatum progeny was assayed for growth rate on potato dextrose agar amended with BOA. Matings were conducted to allow for selection of progeny with lower and higher tolerance of BOA. The results confirmed heritable variation in BOA tolerance in F. circinatum. A subset of differentially tolerant progeny was used for inoculations of growth chamber-grown Zea mays and greenhouse-grown Pinus radiata. No differences were detected in the rate of infection or extent of colonization of Z. mays inoculated with F. circinatum progeny differing in tolerance of BOA. Pitch canker symptoms in inoculated P. radiata trees showed that high BOA-tolerating isolates induced significantly longer lesion lengths than those induced by low BOA-tolerating isolates. Results from this study were consistent with the proposition that F. circinatum evolved from grass-colonizing ancestors and that pathogenicity to pine is a relatively recent evolutionary innovation.

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Survival of Fusarium oxysporum f. sp. lactucae on Crop Residue in Soil

Fusarium oxysporum f. sp. lactucae, the cause of Fusarium wilt of lettuce, can survive on crop residue in soil. Persistence of the pathogen over time will be influenced by the rate at which residue decomposes. We evaluated the effect of drying and fragmenting crop residue on the rate of decomposition and survival of F. oxysporum f. sp. lactucae. In a controlled experiment that represented optimal drying conditions, fragmenting and oven drying infested lettuce taproots at 30°C significantly reduced the frequency of recovery of the pathogen, compared with untreated tissue. However, in a field experiment, drying infested crop residue on the soil surface prior to incorporation did not significantly reduce survival of F. oxysporum f. sp. lactucae after 1 year. Regardless of treatment, there was not a significant decrease in soil inoculum density between 1 and 12 months after residue was incorporated. In a greenhouse experiment, fragmenting crop residue prior to incorporation in pathogen-free soil resulted in significantly higher inoculum densities of F. oxysporum f. sp. lactucae after 1 year. The increase in inoculum levels was associated with a faster rate of residue decomposition, which may be beneficial in the long run but not where lettuce will be replanted within the next year.

Horizontal chromosome transfer and independent evolution drive diversification in Fusarium oxysporum f. sp. fragariae

The genes required for host-specific pathogenicity in Fusarium oxysporum can be acquired through horizontal chromosome transfer (HCT). However, it is unknown if HCT commonly contributes to the diversification of pathotypes. Using comparative genomics and pathogenicity phenotyping, we explored the role of HCT in the evolution of F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry, with isolates from four continents. We observed two distinct syndromes: one included chlorosis ('yellows-fragariae') and the other did not ('wilt-fragariae'). All yellows-fragariae isolates carried a predicted pathogenicity chromosome, 'chrY-frag ', that was horizontally transferred at least four times. chrY-frag was associated with virulence on specific cultivars and encoded predicted effectors that were highly upregulated during infection. chrY-frag was not present in wilt-fragariae; isolates causing this syndrome evolved pathogenicity independently. All origins of F. oxysporum f. sp. fragariae occurred outside of the host's native range. Our data support the conclusion that HCT is widespread in F. oxysporum, but pathogenicity can also evolve independently. The absence of chrY-frag in wilt-fragariae suggests that multiple, distinct pathogenicity chromosomes can confer the same host specificity. The wild progenitors of cultivated strawberry (Fragaria × ananassa) did not co-evolve with this pathogen, yet we discovered several sources of genetic resistance.

Colonization of Wild Blackberry Plants in California by Fusarium oxysporum f. sp. mori

Fusarium oxysporum f. sp. mori, the causal agent of Fusarium wilt of blackberry, was first reported in California and Mexico in 2016. A limited survey of the population revealed this pathogen to be one of the most diverse formae speciales of F. oxysporum. We explored the possibility that strains of F. oxysporum pathogenic to commercial blackberry could also be recovered from wild blackberry (Rubus spp.) in California. For this purpose, wild Rubus species in blackberry nurseries, fruit production fields, and nearby areas were collected between 2017 and 2019. Thirty-four isolates of F. oxysporum were recovered from asymptomatic Rubus armeniacus and Rubus ursinus plants. Based on sequence of the translation elongation factor 1-α, somatic compatibility, and pathogenicity to blackberry, 16 isolates were confirmed as F. oxysporum f. sp. mori. These isolates were associated with three somatic compatibility groups, one of which was first identified in this study. Recovery of the pathogen confirmed that wild blackberry plants can act as a reservoir of inoculum of F. oxysporum f. sp. mori and that it can move from wild blackberry plants to commercial cultivars or vice versa.

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.

The Population of Fusarium oxysporum f. sp. lactucae in California and Arizona

Fusarium wilt of lettuce, caused by Fusarium oxysporum f. sp. lactucae, is now found in all major lettuce producing regions in California and Arizona. The population structure of F. oxysporum f. sp. lactucae in California and Arizona was characterized based on somatic compatibility and sequences of the translation elongation factor 1-α gene (EF-1α) and rDNA intergenic spacer region (IGS). In this study, 170 isolates were tested for somatic compatibility based on heterokaryon formation, using complementary nitrate nonutilizing (nit) mutants. Five subgroups (A to E) of somatic compatibility group 0300 were identified. Isolates associated with the same subgroup had a strong complementation reaction, whereas reactions between isolates of different subgroups were weak or delayed. An isolate from the first known infestation of Fusarium wilt of lettuce in California was associated with subgroup A, which predominated among isolates in our collection. Isolates representative of each subgroup were confirmed to be associated with race 1, based on the reaction of differential lettuce cultivars. It is possible that somatic compatibility subgroups B to E of F. oxysporum f. sp. lactucae were derived from subgroup A, as a consequence of somatic mutations affecting compatibility. If so, subgroups of F. oxysporum f. sp. lactucae may represent an intermediate step in divergence that will lead to clearly separable compatibility groups. Sequences of EF-1α and IGS were both identical for 58 isolates of F. oxysporum f. sp. lactucae that represented all somatic compatibility subgroups and locations from which isolates were obtained, indicating that subgroups were derived from the same clonal lineage (VCG 0300).

Changes of Fusarium oxysporum f.sp. lactucae levels and soil microbial community during soil biosolarization using chitin as soil amendment

Regulatory pressure along with environmental and human health concerns drive the development of soil fumigation alternatives such as soil biosolarization (SBS). SBS involves tarping soil that is at field capacity with a transparent film following amendment with certain organic materials. Heating via the greenhouse effect results in an increase of the soil temperature. The organic amendments can promote microbial activity that can enhance pest inactivation by depleting oxygen, producing biopesticidal fermentation products, and competing with pests. The properties of the organic amendments can heavily influence the type and magnitude of these effects. This study evaluated the viability of chitin as a novel SBS soil amendment to influence soil fungal and bacterial microbial communities, including control of the plant pathogen Fusarium oxysporum f.sp. lactucae (FOL). Changes to FOL and the broader soil microbiota were monitored in response to biosolarization using 0.1% (by dry weight) amendment with chitin (Rootguard). FOL suppression was only observed in chitin amended soils that were incubated at room temperature, not under solarized conditions. Conversely, it decreased solarization efficacy in the upper (0–10 cm) soil layer. The presence of chitin also showed increase in FOL under anaerobic and fluctuating temperature regime conditions. Biosolarization with chitin amendment did exhibit an impact on the overall soil microbial community. The fungal genus Mortierella and the bacterial family Chitinophagaceae were consistently enriched in biosolarized soils with chitin amendment. This study showed low potential FOL suppression due chitin amendment at the studied levels. However, chitin amendment showed a higher impact on the fungal community than the bacterial community. The impact of these microbial changes on crop protection and yields need to be studied in the long-term.

Seasonal Variation in Host Susceptibility to Fusarium Canker in Young Almond Trees

Loss of water that reduces the relative water content (RWC) of bark can occur during processing, cold storage, and planting of bare-root stone fruit trees. In California nurseries and newly planted orchards, this stress can predispose young almond trees (Prunus dulcis) to a canker disease caused primarily by Fusarium species. While reduced bark RWC contributes to disease development, anecdotal observations suggest a seasonal effect on host physiology may also influence disease severity. We evaluated the effect of season and the impact of drying and reduced RWC on susceptibility of almond branch segments excised from orchard trees (cv. Nonpareil) to Fusarium acuminatum, Fusarium avenaceum, Fusarium brachygibbosum, and Fusarium californicum sp. nov. With lesion size as the criterion, excised inoculated branch segments were most susceptible in spring, of intermediate susceptibility during winter dormancy, and least susceptible during summer and fall. Consistent with an earlier study, branches with RWC between 80 and 85% yielded lesions that were significantly larger than lesions from branches with bark that was above or below that range. However, the effect of reduced bark moisture on lesion size was only apparent in the spring. These results affirm the importance of avoiding conditions that diminish moisture status in bare-root almond trees in Fusarium canker disease management, especially during transport and planting operations in the spring, a period of high physiological vulnerability. California nurseries apply fungicides to bare-root trees prior to cold storage to reduce "mold" growth. Of eight fungicides currently registered for use on almond trees, fludioxonil (Scholar), fluopyram/trifloxystrobin (Luna Sensation), and fluxapyroxad/pyraclostrobin (Merivon) were most inhibitory to in vitro mycelial growth of F. acuminatum, F. avenaceum, and F. brachygibbosum. However, our almond branch disease assay did not demonstrate preventive or curative fungicide action against infections by F. acuminatum or F. avenaceum.

Infection of the Native California Grass, Bromus carinatus, by Fusarium circinatum, the Cause of Pitch Canker in Pines

At Point Reyes National Seashore in California, Fusarium circinatum, the causal agent of pitch canker in pines, was isolated from Pinus muricata, the California native grass, Bromus carinatus, and the introduced grass, Holcus lanatus. All grass plants from which F. circinatum was isolated were symptomless. Pathogenicity of grass isolates was confirmed by inoculation of P. radiata trees, which developed symptoms similar to trees inoculated with a pine isolate of F. circinatum. Isolates from grasses were somatically compatible with isolates recovered from symptomatic pines. B. carinatus grown in a growth chamber was inoculated with a green fluorescent protein-expressing strain of F. circinatum. Segments of inoculated leaves were incubated in moist chambers; after 1 to 2 days, sporulating hyphae were observed growing from leaf tissue. Spores of F. circinatum removed from B. carinatus leaves were confirmed to be fluorescent when illuminated with ultraviolet light. These results raise the possibility that B. carinatus cryptically infected by F. circinatum may be a source of propagules capable of infecting pines.

Cryptic Infection and Systemic Colonization of Leguminous Crops by Verticillium dahliae, the Cause of Verticillium Wilt

Verticillium dahliae, the cause of Verticillium wilt, is a widespread pathogen that affects many crops in California and throughout the world. Cover cropping with leguminous species is often integrated into a rotation scheme for its contribution to soil nitrogen, and can contribute to management of Verticillium wilt provided the chosen crop does not support development of V. dahliae. Seven cool season legumes (faba bean, bell bean, field pea, hairy vetch, common vetch, purple vetch, and woollypod vetch), and three warm season legumes (sesbania, sunn hemp, and black-eyed pea) were evaluated as hosts for reproductive growth of V. dahliae. All 10 legumes were colonized by V. dahliae, while remaining symptomless, when subjected to a root-dip inoculation. Similar results were obtained when plants were grown in infested potting soil, albeit with a lower frequency of infection than in root-dip assays. All tested legumes were also infected in field trials, with the exception of bell bean. Overall, warm season legumes sustained higher rates of infection than cool season legumes. Common vetch was the most extensively colonized of the cool season legumes. Based on the results of this study, legumes may not be an appropriate rotation crop in fields where Verticillium wilt is a problem.

Using Game Theory to Understand Systemic Acquired Resistance as a Bet-Hedging Option for Increasing Fitness When Disease Is Uncertain

Systemic acquired resistance (SAR) is a mechanism through which plants may respond to initial challenge by a pathogen through activation of inducible defense responses, thereby increasing resistance to subsequent infection attempts. Fitness costs are assumed to be incurred by plants induced for SAR, and several studies have attempted to quantify these costs. We developed a mathematical model, motivated by game-theoretic concepts, to simulate competition between hypothetical plant populations with and without SAR to examine conditions under which the phenomenon of SAR may have evolved. Data were gathered from various studies on fitness costs of induced resistance on life history traits in different plant hosts and scaled as a proportion of the values in control cohorts in each study (i.e., healthy plants unprimed for SAR). With unprimed healthy control plants set to a fitness value of 1, primed healthy plants incurred a fitness cost of about 10.4% (0.896, n = 157), primed diseased plants incurred a fitness cost of about 15.5% (0.845, n = 54), and unprimed diseased plants incurred a fitness cost of about 28.9% (0.711, n = 69). Starting from a small proportion of the population (0.5%) and competing against a population with constitutive defenses alone in stochastic simulations, the SAR phenotype almost always dominated the population after 1000 generations when the probability of disease was greater than or equal to 0.5 regardless of the probability for priming errors.

Effect of Planting Date and Inoculum Density on Severity of Fusarium Wilt of Lettuce in California

Seven lettuce cultivars were transplanted into a field infested with Fusarium oxysporum f. sp. lactucae (causal agent of Fusarium wilt of lettuce) in August and September of 2014, 2015, and 2016. For moderately susceptible cultivars, 1- or 2-week differences in planting date had a significant effect on severity of Fusarium wilt. In growth chamber experiments, cultivars of moderate susceptibility were maintained in a growth chamber under cool conditions (23/18°C), and a subset of plants was transferred to a warm chamber (33/23°C) for 1 week, at weekly intervals after transplanting. Plants exposed to high temperatures at 2 and 3 weeks after transplanting (WAT) had more severe symptoms of Fusarium wilt than those exposed at 4 WAT. In October 2015, April 2016, August 2016, and August 2017, moderately susceptible cultivars were planted into field soil with an inoculum density gradient. Moderately susceptible cultivars were little affected by Fusarium wilt where inoculum densities of F. oxysporum f. sp. lactucae were <125 per gram of soil, even in warm planting windows. Adjusting planting dates to avoid high temperatures during a critical stage of growth and maintaining low inoculum density in soil can contribute to management of Fusarium wilt in moderately susceptible lettuce cultivars.

Transmission of Fusarium oxysporum f. sp. fragariae Through Stolons in Strawberry Plants

Fusarium wilt of strawberry, caused by the soilborne pathogen Fusarium oxysporum f. sp. fragariae, is a growing threat to the strawberry industry worldwide. Symptoms of the disease typically include stunting, wilting, crown discoloration, and eventual plant death. When Fusarium wilt was discovered in California, the disease was not known to occur anywhere else in North America. Long distance movement of the pathogen would most likely occur through transport of infected plants, which seems plausible if strawberry plants can sustain infections without showing symptoms of disease. The results of this study document that F. oxysporum f. sp. fragariae can move through stolons of infected mother plants and colonize first-generation daughter plants. The pathogen can also move through stolons from first to second-generation daughter plants. Daughter plants of both generations were always symptomless. The pathogen was recovered from both roots and petioles of infected daughter plants. Similar results were obtained for two cultivars known to be susceptible to Fusarium wilt, Albion and Monterey. Transmission through stolons from mother to daughter plants also occurred in the resistant cultivar, San Andreas, but less frequently than in Albion and Monterey.

Persistence of Fusarium oxysporum f. sp. fragariae in Soil Through Asymptomatic Colonization of Rotation Crops

Asymptomatic plant colonization is hypothesized to enhance persistence of pathogenic forms of Fusarium oxysporum. However, a correlation between pathogen populations on living, asymptomatic plant tissues and soilborne populations after tillage has not been demonstrated. Living and dead tissues of broccoli, lettuce, spinach, wheat, cilantro, raspberry, and strawberry plants grown in soil infested with F. oxysporum f. sp. fragariae (the cause of Fusarium wilt of strawberry) were assayed to quantify the incidence of infection and extent of colonization by this pathogen. All crops could be infected by F. oxysporum f. sp. fragariae but the extent of colonization varied between plant species. Pathogen population densities on nonliving crown tissues incorporated into the soil matrix were typically greater than those observed on living tissues. Crop-dependent differences in the inoculum density of F. oxysporum f. sp. fragariae in soil were only observed after decomposition of crop residue. Forty-four weeks after plants were incorporated into the soil, F. oxysporum f. sp. fragariae soil population densities were positively correlated with population densities on plant tissue fragments recovered at the same time point. Results indicate that asymptomatic colonization can have a significant, long-term impact on soilborne populations of Fusarium wilt pathogens. Cultural practices such as crop rotation should be leveraged to favor pathogen population decline by planting hosts that do not support extensive population growth on living or decomposing tissues.

Detection of Fusarium oxysporum f. sp. fragariae from Infected Strawberry Plants

Isolates of the Fusarium oxysporum species complex have been characterized as plant pathogens that commonly cause vascular wilt, stunting, and yellowing of the leaves in a variety of hosts. F. oxysporum species complex isolates have been grouped into formae speciales based on their ability to cause disease on a specific host. F. oxysporum f. sp. fragariae is the causal agent of Fusarium wilt of strawberry and has become a threat to production as fumigation practices have changed in California. F. oxysporum f. sp. fragariae is polyphyletic and limited genetic markers are available for its detection. In this study, next-generation sequencing and comparative genomics were used to identify a unique genetic locus that can detect all of the somatic compatibility groups of F. oxysporum f. sp. fragariae identified in California. This locus was used to develop a TaqMan quantitative polymerase chain reaction assay and an isothermal recombinase polymerase amplification (RPA) assay that have very high sensitivity and specificity for more than 180 different isolates of the pathogen tested. RPA assay results from multiple field samples were validated with pathogenicity tests of recovered isolates.

The Effect of pH on Spore Germination, Growth, and Infection of Strawberry Roots by Fusarium oxysporum f. sp. fragariae, Cause of Fusarium wilt of Strawberry

Previous work has shown that raising the pH of acidic soil to near neutrality can reduce the incidence of Fusarium wilt. The basis for this effect has not been established. The present study assessed effects of pH on spore germination, growth, and infection of strawberry roots by Fusarium oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry. There was not a significant effect of pH (5 versus 7) on the rate of spore germination at either 20 or 25°C for any of the three tested isolates (one representative of each clonal lineage of F. oxysporum f. sp. fragariae found in California). Likewise, pH did not have a significant effect on fungal growth at 20°C. At 25°C, two isolates grew faster at pH 7 than at pH 5. Growth of the third isolate was unaffected by the difference in pH. For the strawberry cultivar Albion, the frequency of root infection was significantly higher for plants grown in acidified soil (near pH 5) than for plants grown in soil near neutrality. The higher frequency of root infection in acidified soil was associated with a lower level of microbial activity, as measured by hydrolysis of fluorescein diacetate.

Effect of management of organic wastes on inactivation of Brassica nigra and Fusarium oxysporum f.sp. lactucae using soil biosolarization

BACKGROUND

Soil biosolarization is a promising alternative to conventional fumigation. Volatile fatty acids (VFAs) produced in the soil through fermentation of amended organic matter can affect pest inactivation during biosolarization. The objective was to determine how soil amended with organic wastes that were partially stabilized through either composting or anaerobic digestion affected the inactivation of Brassica nigra (BN; a weed) and Fusarium oxysporum f. sp. lactucae (FOL; a phytopathogenic fungus).

RESULTS

The mortality of BN seeds in the biosolarized soil was 12% higher than in the solarized soil, although this difference was not significant. However, a significant correlation between BN mortality and VFA accumulation was observed. The number of FOL colony-forming units (CFU) in solarized samples at 5 cm was 34 CFU g^-1 of soil, whereas in the biosolarized samples levels were below the limit of quantification. At 15 cm, these levels were 100 CFU g^-1 for solarized samples and < 50 CFU g^-1 of soil for the biosolarized samples. Amendment addition positively affected the organic matter and potassium content after the solarization process.

CONCLUSION

The organic waste stabilization method can impact downstream biosolarization performance and final pest inactivation levels. This study suggests that organic waste management practices can be leveraged to improve pest control and soil quality. © 2018 Society of Chemical Industry.

Fusarium oxysporum f. sp. mori, a New Forma Specialis Causing Fusarium Wilt of Blackberry

Fusarium oxysporum has recently been identified as the cause of a wilt disease affecting blackberry in California and Mexico. Thirty-six isolates of F. oxysporum obtained from symptomatic blackberry plants in California and Mexico were comprised of nine distinct somatic compatibility groups (SCGs). Phylogenetic analysis of a concatenated data set, consisting of sequences of the translation elongation factor 1-α and β-tubulin genes and the intergenic spacer of the ribosomal DNA, identified nine three-locus sequence types, each of which corresponded to an SCG. Six SCGs were present only in California, two only in Mexico, and one in both California and Mexico. An isolate associated with the most common SCG in California was tested for pathogenicity on blueberry, raspberry, strawberry, and lettuce. All blueberry, raspberry, and lettuce plants that were inoculated remained healthy, but two of the five strawberry cultivars tested developed symptoms. The three strawberry cultivars that were resistant to the blackberry pathogen were also resistant to F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry. We propose to designate strains of F. oxysporum that are pathogenic to blackberry as Fusarium oxysporum f. sp. mori forma specialis nov.

Fusarium oxysporum and the Fusarium Wilt Syndrome

The Fusarium oxysporum species complex (FOSC) comprises a multitude of strains that cause vascular wilt diseases of economically important crops throughout the world. Although sexual reproduction is unknown in the FOSC, horizontal gene transfer may contribute to the observed diversity in pathogenic strains. Development of disease in a susceptible crop requires F. oxysporum to advance through a series of transitions, beginning with spore germination and culminating with establishment of a systemic infection. In principle, each transition presents an opportunity to influence the risk of disease. This includes modifications of the microbial community in soil, which can affect the ability of pathogen propagules to survive, germinate, and infect plant roots. In addition, many host attributes, including the composition of root exudates, the structure of the root cortex, and the capacity to recognize and respond quickly to invasive growth of a pathogen, can impede development of F. oxysporum.

The Population of Fusarium oxysporum f. sp. fragariae, Cause of Fusarium Wilt of Strawberry, in California

The objectives of this study were to investigate the structure of the population of Fusarium oxysporum f. sp. fragariae in California and to evaluate methods for its detection. Fifty-nine isolates of F. oxysporum f. sp. fragariae were obtained from diseased strawberry plants and their identity was confirmed by pathogenicity testing. The full nuclear ribosomal intergenic spacer (IGS) and elongation factor 1-α gene (EF-1α) were amplified by polymerase chain reaction (PCR) and sequenced to elucidate phylogenetic relationships among isolates. IGS and EF-1α sequences revealed three main lineages, which corresponded to three somatic compatibility groups. Primers designed to detect F. oxysporum f. sp. fragariae in Japan amplified a 239-bp product from 55 of 59 California isolates of F. oxysporum f. sp. fragariae and from no nonpathogenic isolates of F. oxysporum. The sequence of this PCR product was identical to the sequence obtained from F. oxysporum f. sp. fragariae isolates in Japan. Intensive sampling at two locations in California showed results of tests based on PCR and somatic compatibility to be in agreement for 97% (257 of 264) of isolates tested. Our findings revealed considerable diversity in the California population of F. oxysporum f. sp. fragariae, and indications that horizontal gene transfer may have occurred.