Development of Recombinase Polymerase Amplification-Lateral Flow Dipstick (RPA-LFD) as a Rapid On-Site Detection Technique for Fusarium oxysporum

Fusarium oxysporum can cause many important plant diseases worldwide, such as crown rot, wilt, and root rot. During the development of strawberry crown rot, this pathogenic fungus spreads from the mother plant to the strawberry seedling through the stolon, with obvious characteristics of latent infection. Therefore, the rapid and timely detection of F. oxysporum can significantly help achieve effective disease management. Here, we present a protocol for the recombinase polymerase amplification- lateral flow dipstick (RPA-LFD) detection technique for the rapid detection of F. oxysporum on strawberry, which only takes half an hour. A significant advantage of our RPA-LFD technique is the elimination of the involvement of professional teams and laboratories, which qualifies it for field detection. We test this protocol directly on plant samples with suspected infection by F. oxysporum in the field and greenhouse. It is worth noting that this protocol can quickly, sensitively, and specifically detect F. oxysporum in soils and plants including strawberry. Key features • This protocol is used to detect whether plants such as strawberry are infected with F. oxysporum. • This protocol has potential for application in portable nucleic acid detection. • It can complete the detection of samples in the field within 30 min.

First Report of Neopestalotiopsis rosae Causing Crown and Root Rot of Strawberry in California

Strawberry production in California represents over 38,000 acres with an annual farm value of $1.99 billion. Strawberry dieback was observed in February of 2021 in the Salinas Valley in central California. Disease symptoms included dead and dying 'Maverick' strawberry plants with necrotic lesions and black discoloration of the crown, root cortex, epidermis, and vascular tissues. Disease incidence was estimated to be 60% of a 20-acre field. The causal agent was isolated from five randomly selected symptomatic plants by surface disinfesting symptomatic crowns and roots in 1% sodium hypochlorite for 30 s, rinsed twice in sterile water for 30 s then placed on 3.7% potato dextrose agar (PDA) Petri dishes amended with 100 mg/L streptomycin, and then incubated for 7 days at 24°C under a 12-h photoperiod. Consistent white cottony fungal colonies were hyphal tip transferred to fresh PDA dishes and incubated as above for morphological and genetic comparisons. Black acervuli developed 7 to 9 days after incubation. Conidia were ellipsoidal, measuring 25 to 30 × 7.5 to 10 µm (average 26.8 × 9.2 µm, n = 30), with five cells. Apical and basal cells were hyaline, and the three median cells were versicolorous brown, with a single, straight, centric basal appendage and 3 to 4 flexuous apical appendages. Colony diameter averaged 90 mm in 7 days. Based on colony and conidial characters, the fungus was tentatively identified as a species of Neopestalotiopsis (Maharachchikumbura et al. 2014). Total genomic DNA was extracted from three axenic cultures using the Invitrogen Easy-DNA kit. Three genetic loci were PCR amplified and sequenced: internal transcribed spacer (ITS), beta-tubulin (BT), and translation elongation factor 1-alpha (TEF) utilizing the primer pairs ITS1/ITS4, T1/Bt2a, and EF1-688F/EF1-1251R, respectively (White et al. 1990, O'Donnell and Cigelnik 1997, Glass and Donaldson 1995, and Alves et al. 2008). A BLASTn search of NCBI showed 99.6% identity (495/497 bases; OM942910-OM942912) with the type specimen of Neopestalotiopsis rosae CBS 101057 for the ITS locus. Both BT (765/765 bases, OM964802-OM964804) and TEF (475/475 bases; OM964799-OM964801) sequences were 100% identical to CBS 101057. Conidia of isolate PAR027 were scraped from the surface of 14-day-old PDA Petri dishes and inoculated (1 × 106 spores/mL: 2 mL/plant) to four apparently healthy strawberry transplant roots of the cultivar 'Monterey' in 'sunshine mix' potting soil. Two control plants were inoculated with sterile water. The experiment was conducted twice. Strawberry plants were maintained in a hoop house for four weeks, after which dieback and wilt symptoms resembled the symptoms observed in the field. Control plants remained asymptomatic and no pathogens were isolated. Fungal recovery from inoculated plants morphologically matched the original inoculum; thus, Koch's postulates was satisfied. To our knowledge, this is the first report of N. rosae causing crown and root rot disease of strawberry in California. Previously, N. rosae has been reported to cause serious decline of strawberry plants in Florida and several countries (Baggio et al. 2021, Rebollar-Alviter et al. 2020, Wu et al. 2021, Sun et al. 2021). Correct identification of the causal agent provides a proper foundation to identify control strategies for this emerging disease, which has the potential to become a significant problem for strawberry growers in the Salinas Valley of California.

TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum

BACKGROUND

Fusarium crown rot is major disease in wheat. However, the wheat defense mechanisms against this disease remain poorly understood.

RESULTS

Using tandem mass tag (TMT) quantitative proteomics, we evaluated a disease-susceptible (UC1110) and a disease-tolerant (PI610750) wheat cultivar inoculated with Fusarium pseudograminearum WZ-8A. The morphological and physiological results showed that the average root diameter and malondialdehyde content in the roots of PI610750 decreased 3 days post-inoculation (dpi), while the average number of root tips increased. Root vigor was significantly increased in both cultivars, indicating that the morphological, physiological, and biochemical responses of the roots to disease differed between the two cultivars. TMT analysis showed that 366 differentially expressed proteins (DEPs) were identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment in the two comparison groups, UC1110_3dpi/UC1110_0dpi (163) and PI610750_3dpi/PI610750_0dpi (203). It may be concluded that phenylpropanoid biosynthesis (8), secondary metabolite biosynthesis (12), linolenic acid metabolites (5), glutathione metabolism (8), plant hormone signal transduction (3), MAPK signaling pathway-plant (4), and photosynthesis (12) contributed to the defense mechanisms in wheat. Protein-protein interaction network analysis showed that the DEPs interacted in both sugar metabolism and photosynthesis pathways. Sixteen genes were validated by real-time quantitative polymerase chain reaction and were found to be consistent with the proteomics data.

CONCLUSION

The results provided insight into the molecular mechanisms of the interaction between wheat and F. pseudograminearum.

Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BACKGROUND

Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops.

RESULTS

In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection.

CONCLUSIONS

Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

Map-based cloning identifies velvet A as a critical component of virulence in Fusarium pseudograminearum during infection of wheat heads

Although better known as a pathogen of wheat stem bases, Fusarium pseudograminearum also causes Fusarium head blight. A natural isolate of F. pseudograminearum was identified that showed severely reduced virulence towards wheat heads and a map-based cloning approach was undertaken to identify the genetic basis of this phenotype. Using a population of 95 individuals, a single locus on chromosome 1 was shown to be responsible for the low virulence. Fine mapping narrowed the region to just five possible SNPs of which one was in the F. pseudograminearum homologue of velvet A. Knockout mutants of velvet A, which were non-pathogenic towards wheat, confirmed that velvet A regulates virulence in this pathogen. The mutation in velvet A was only found in a single field isolate and the origin of the mutation is unknown.

Speed breeding for multiple quantitative traits in durum wheat

BACKGROUND

Plant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named 'speed breeding' was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F₂ population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F₃ progeny derived from 100 'selected' and 100 'unselected' F₂ individuals.

RESULTS

Transgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F₂ population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between 'selected' and 'unselected' F₃ families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed.

CONCLUSIONS

The novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.