Disease Resistance Mechanisms Research Articles

Genome-wide association study for adult plant resistance to yellow rust in spring bread wheat (Triticum aestivum L.)

Yellow rust, caused by Puccinia striiformis f. sp. tritici, is a common and serious fungal disease of wheat (Triticum aestivum L.) all over the world and particularly in the Central and West Asia and North Africa region. To identify effective yellow rust resistance loci, genome-wide association study (GWAS) was performed using 196 bread wheat genotypes based on 10,477 single nucleotide polymorphisms markers. Adult plants were evaluated under field conditions for resistance to yellow rust for 2 years (2014–2015) at ICARDA station, Marchouch, Morocco. Out of the 196 genotypes, 85 genotypes (43.37%) were resistant, 22 genotypes (11.22%) were moderately resistant, 13 genotypes (6.63%) were moderately susceptible, 48 genotypes (24.49%) were moderately susceptible to susceptible and 28 genotypes (14.29%) were susceptible to Puccinia striiformis f. sp. tritici. GWAS using mixed linear model identified 23 markers on chromosomes 2A, 2B, 2D and 7B significantly associated with adult plant resistance at false discovery rate (FDR-adjusted P ≤ 0.05). Of which, three markers were within 10 wheat functional genes involved in several plant disease resistance and defense mechanism. Five of the reported functional genes are annotated as disease resistance proteins with nucleotide-binding site leucine repeat domains. BLAST analysis confirmed that YrR61 and Yr17 were mostly the candidate genes linked to the marker Tdurum_contig29983_490 on chromosome 2A. Moreover, markers identified on chromosome 7B and Kukri_c12648_434 on 2D were not mapped within any of previously reported gene/QTL region hence, representing novel resistance loci for Pst and needs to be confirmed using an allelism test.

Comparative transcriptome profiling identifies maize line specificity of fungal effectors in the maize-Ustilago maydis interaction.

The biotrophic pathogen Ustilago maydis causes smut disease on maize (Zea mays) and induces the formation of tumours on all aerial parts of the plant. Unlike in other biotrophic interactions, no gene-for-gene interactions have been identified in the maize-U.maydis pathosystem. Thus, maize resistance to U.maydis is considered a polygenic, quantitative trait. Here, we study the molecular mechanisms of quantitative disease resistance (QDR) in maize, and how U.maydis interferes with its components. Based on quantitative scoring of disease symptoms in 26 maize lines, we performed an RNA sequencing (RNA-Seq) analysis of six U.maydis-infected maize lines of highly distinct resistance levels. The different maize lines showed specific responses of diverse cellular processes to U.maydis infection. For U. maydis, our analysis identified 406 genes being differentially expressed between maize lines, of which 102 encode predicted effector proteins. Based on this analysis, we generated U.maydis CRISPR/Cas9 knock-out mutants for selected candidate effector sets. After infections of different maize lines with the fungal mutants, RNA-Seq analysis identified effectors with quantitative, maize line-specific virulence functions, and revealed auxin-related processes as a possible target for one of them. Thus, we show that both transcriptional activity and virulence function of fungal effector genes are modified according to the infected maize line, providing insights into the molecular mechanisms underlying QDR in the maize-U.maydis interaction.

Inoculation with arbuscular mycorrhizal fungus modulates defense-related genes expression in banana seedlings susceptible to wilt disease

ABSTRACT Banana as an important economic crop worldwide, often suffers from serious damage caused by Fusarium oxysporum f. sp. Cubense. Arbuscular mycorrhizal (AM) fungi have been considered as one of the promising plant biocontrol agents in preventing from root pathogens. This study examined the effect of AM fungal inoculation on plant growth and differential expressions of growth- and defense-related genes in banana seedlings. Tissue-cultured seedlings of Brazilian banana (Musa acuminate Cavendish cv. Brail) were inoculated with AM fungus (Rhizophagus irregularis, Ri), and developed good mycorrhizal symbiosis from 4 to 11 weeks after inoculation with an infection rate up to 71.7% of the roots system. Microbial abundance revealed that Ri abundance in banana roots was 1.85×106 copies/ml at 11 weeks after inoculaiton. Inoculation improved plant dry weights by 47.5, 124, and 129% for stem, leaf, and the whole plant, respectively, during phosphate depletion. Among a total of 1411 differentially expressed genes (DEGs) obtained from the transcriptome data analysis, genes related to plant resistance (e.g. POD, PAL, PYR, and HBP-1b) and those related to plant growth (e.g. IAA, GH3, SAUR, and ARR8) were up-regulated in AM plants. This study demonstrates that AM fungus effectively promoted the growth of banana plants and induced defense-related genes which could help suppress wilt disease. The outcomes of this study form a basis for further study on the mechanism of banana disease resistance induced by AM fungi.

Applications of liquid biopsy in the Pharmacological Audit Trail for anticancer drug development.

Anticancer drug development is a costly and protracted activity, and failure at late phases of clinical testing is common. We have previously proposed the Pharmacological Audit Trail (PhAT) intended to improve the efficiency of drug development, with a focus on the use of tumour tissue-based biomarkers. Blood-based 'liquid biopsy' approaches, such as targeted or whole-genome sequencing studies of plasma circulating cell-free tumour DNA (ctDNA) and circulating tumour cells (CTCs), are of increasing relevance to this drug development paradigm. Liquid biopsy assays can provide quantitative and qualitative data on prognostic, predictive, pharmacodynamic and clinical response biomarkers, and can also enable the characterization of disease evolution and resistance mechanisms. In this Perspective, we examine the promise of integrating liquid biopsy analyses into the PhAT, focusing on the current evidence, advances, limitations and challenges. We emphasize the continued importance of analytical validation and clinical qualification of circulating tumour biomarkers through prospective clinical trials.

Identification of long noncoding RNAs involved in resistance to downy mildew in Chinese cabbage

Brassica downy mildew, a severe disease caused by Hyaloperonospora brassicae, can cause enormous economic losses in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Although some research has been reported recently concerning the underlying resistance to this disease, no studies have identified or characterized long noncoding RNAs involved in this defense response. In this study, using high-throughput RNA sequencing, we analyzed the disease-responding mRNAs and long noncoding RNAs in two resistant lines (T12–19 and 12–85) and one susceptible line (91–112). Clustering and Gene Ontology analysis of differentially expressed genes (DEGs) showed that more DEGs were involved in the defense response in the two resistant lines than in the susceptible line. Different expression patterns and proposed functions of differentially expressed long noncoding RNAs among T12–19, 12–85, and 91–112 indicated that each has a distinct disease response mechanism. There were significantly more cis- and trans-functional long noncoding RNAs in the resistant lines than in the susceptible line, and the genes regulated by these RNAs mostly participated in the disease defense response. Furthermore, we identified a candidate resistance-related long noncoding RNA, MSTRG.19915, which is a long noncoding natural antisense transcript of a MAPK gene, BrMAPK15. Via an agroinfiltration-mediated transient overexpression system and virus-induced gene silencing technology, BrMAPK15 was indicated to have a greater ability to defend against pathogens. MSTRG.19915-silenced seedlings showed enhanced resistance to downy mildew, probably because of the upregulated expression of BrMAPK15. This research identified and characterized long noncoding RNAs involved in resistance to downy mildew, laying a foundation for future in-depth studies of disease resistance mechanisms in Chinese cabbage.

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress.

Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol. A striking lack of information about dirigent genes in cucurbitaceae plants underscores the importance of functional characterization. In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignification and pathogen resistance activities. We also determined their organ-specific expression levels in three species revealing preferential expression in root and leaves. Furthermore, the number of CmDIR (CmDIR1, 6, 7 and 12) and ClDIR (ClDIR2, 5, 8, 9 and 17) genes exhibited higher expression in resistant cultivars after powdery mildew (PM) inoculation. In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.

Red rot of sugarcane (Colletotrichum falcatumWent)

AbstractRed rot of sugarcane was recorded more than 100 years before in Java, India, Argentina, USA and other countries, and it is one of the most devastating diseases of sugarcane. Since the cultivated sugarcane (Saccharum officinarum) has failed across the countries, systematic inter-specific hybridization betweenS. officinarumand the wild speciesS. spontaneumreferred as ‘nobilization’ was done to develop resistant varieties and the disease was managed in most of the countries. However, in the countries especially in Asia, varietal breakdown to red rot caused severe epiphytotics, by which the resistant varieties failed in the field at regular intervals. New pathogenic strains ofColletotrichum falcatumwith higher virulence were found responsible for varietal breakdown in sugarcane. Extensive cultivation of a single variety over large areas led to extensive crop damages due to ‘vertifolia’ effect in different decades in India. The current epiphytotic on the ruling variety Co 0238 has caused loss of more than one billion US dollars in the current season in the country. Detailed studies were done on pathogenic variation, epidemiology, screening methods, disease resistance mechanism, identifying effectors, pathogenicity determinants, antifungal genes and transgenics. Recently, complete genome and transcriptomes ofC. falcatumwere sequenced and pathogenicity hot spots and candidate secreted effector proteins were identified and this will further help to identify the candidate genes for further genetic manipulation. In spite of poor understanding on inheritance of resistance toC. falcatumin sugarcane, new varieties with red rot resistance were developed and deployed after each of the epiphytotic to save the crop. Further, other management practices including bioagents, chemicals and inducers were attempted and improved efficacy by mechanized sett treatment showed promising results to manage the disease under field conditions.

The role of AcPGIP in the kiwifruit (Actinidia chinensis) response to Botrytis cinerea.

Kiwifruit (Actinidia chinensis) is rich in nutritional and medicinal value. However, the organism responsible for grey mould, Botrytis cinerea, causes great economic losses and food safety problems to the kiwifruit industry. Understanding the molecular mechanism underlying postharvest kiwifruit responses to B. cinerea is important for preventing grey mould decay and enhancing resistance breeding. Kiwifruit cv. 'Hongyang' was used as experimental material. The AcPGIP gene was cloned and virus-induced gene silencing (VIGS) was used to explore the function of the polygalacturonase inhibiting protein (PGIP) gene in kiwifruit resistance to B. cinerea. Virus-induced silencing of AcPGIP resulted in enhanced susceptibility of kiwifruit to B. cinerea. Antioxidant enzymes, secondary metabolites and endogenous hormones were analysed to investigate kiwifruit responses to B. cinerea infection. Kiwifruit effectively activated antioxidant enzymes and secondary metabolite production in response to B. cinerea, which significantly increased Indole-3-acetic acid (IAA), gibberellin 3 (GA3) and abscisic acid (ABA) content relative to those in uninfected fruit. Silencing of AcPGIP enabled kiwifruit to quickly activate hormone-signaling pathways through an alternative mechanism to trigger defence responses against B. cinerea infection. These results expand our understanding of the regulatory mechanism for disease resistance in kiwifruit; further, they provide gene-resource reserves for molecular breeding of kiwifruit for disease resistance.

Receptor-Like Kinase (RLK) as a candidate gene conferring resistance to Hemileia vastatrix in coffee

The biotrophic fungus Hemileia vastatrix causes coffee leaf rust (CLR), one of the most devastating diseases in Coffea arabica . Coffee, like other plants, has developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs) have been identified in certain plants as candidates for resistance ( R ) genes or membrane receptors that activate the R genes. The RGAs identified in different plants possess conserved domains that play specific roles in the fight against pathogens. Despite the importance of RGAs, in coffee plants these genes and other molecular mechanisms of disease resistance are still unknown. This study aimed to sequence and characterize candidate genes from coffee plants with the potential for involvement in resistance to H. vastatrix . Sequencing was performed based on a library of bacterial artificial chromosomes (BAC) of the coffee clone ‘Híbrido de Timor’ (HdT) CIFC 832/2 and screened using a functional marker. Two RGAs, HdT_LRR_RLK1 and HdT_LRR_RLK2, containing the motif of leucine-rich repeat-like kinase (LRR-RLK) were identified. Based on the presence or absence of the HdT_LRR_RLK2 RGA in a number of differential coffee clones containing different combinations of the rust resistance gene, these RGAs did not correspond to any resistance gene already characterized (SH1-9). These genes were also analyzed using qPCR and demonstrated a major expression peak at 24 h after inoculation in both the compatible and incompatible interactions between coffee and H. vastatrix . These results are valuable information for breeding programs aimed at developing CLR-resistant cultivars, in addition to enabling a better understanding of the interactions between coffee and H. vastatrix .

Bacillus subtilis KLBC BS6 induces resistance and defence-related response against Botrytis cinerea in blueberry fruit

The potential biocontrol strain Bacillus subtilis KLBC BS6 was isolated from blueberry rhizosphere soil, and its efficacy for controlling grey mould caused by Botrytis cinerea in postharvest blueberry fruit and the underlying possible disease resistance mechanisms were investigated. Treatment with B. subtilis KLBC BS6 was expected to inhibit the mycelial growth and conidial germination of B.cinerea in vitro. The incidence of grey mould in blueberry fruit treated with B. subtilis KLBC BS6 (and inoculated with B. cinerea) was decreased compared with that in the control fruit after 4 days of incubation, regardless of the preventive or curative nature of the treatment. Moreover, preventive treatment was more effective than the curative one in controlling of grey mould-induced decay. In B. subtilis KLBC BS6-treated blueberry fruit, the activities of disease resistance-related enzymes (chitinase, phenylalanine ammonia lyase, peroxidase, and polyphenol oxidase) were significantly enhanced. Furthermore, compared to the control fruit, the B. subtilis KLBC BS6-treated blueberry fruit exhibited unimpaired internal fruit quality and maintained high titratable acidity and ascorbic acid content. Thus, B. subtilis KLBC BS6 is a suitable biocontrol agent for prolonging the postharvest shelf-life of blueberry fruit and other horticultural products.

Silica nanoparticles enhance disease resistance in Arabidopsis plants

In plants, pathogen attack can induce an immune response known as systemic acquired resistance (SAR) that protects against a broad spectrum of pathogens. In the search for safer agrochemicals, silica nanoparticles (SiO2-NPs, food additive E551) have recently been proposed as a new tool. However, initial results are controversial, and the molecular mechanisms of SiO2-NP-induced disease resistance are unknown. Here, we show that SiO2-NPs, as well as soluble orthosilicic acid (Si(OH)4), can induce SAR in a dose-dependent manner, that involves the defence hormone salicylic acid. Nanoparticle uptake and action occurred exclusively through stomata (leaf pores facilitating gas exchange) and involved extracellular adsorption in leaf air spaces of the spongy mesophyll. In contrast to treatment with SiO2-NPs, induction of SAR by Si(OH)4 was problematic, since high concentrations caused stress. We conclude that SiO2-NPs have the potential to serve as an inexpensive, highly efficient, safe, and sustainable alternative for plant disease protection.

Metabolism of the cutin and wax of plants and their disease resistance mechanisms

As a type of secondary metabolites produced by plants during long-term ecological adaptation, cutin and wax are widely involved in many resistance physiological processes including stress defense and resistance to pests and diseases, playing critical roles in the plant-pathogen interaction, thus becoming an important part of plant disease resistance mechanism. With the development of molecular biology, there is an increasing understanding on the cutin and wax metabolism and their mechanisms against fungal disease in plant. With prior researches mainly focused on the constitutive resistance and inducible resistance of plant cutin and wax, the present study, with a review of the research progress achieved on the plant cutin and wax biosynthesis and its disease resistance mechanism, is aimed to put forward prospects for future research. It was concluded that (1) as the main components of the cuticle, the first line of defense for plants against pathogen infection, cutin and wax play a critical role in physical resistance (physical barrier) and chemical resistance (bacteriostasis) as constitutive resistance components, (2) They can also play the role of inducible resistance components and (3) in addition to being the main component of the cuticle to exert physical resistance, the inducible cutin and wax component can also act as a signal molecule or inducer to activate downstream resistance reactions and exert its chemical resistance function. In the future, the research concerning cutin and wax can be focused on an in-depth explanation of the mechanism of cutin and wax inducible resistance, so as to further enrich the theoretical system of plant chemical ecology. In addition, cutin and wax biopesticides (plant immunity inducers) can be developed based on the inducible resistance of cutin and wax to provide new insight for the plant diseases control. [Ch, 1 fig. 71 ref.]

Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease

BackgroundLate blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis.ResultsA total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot.ConclusionsWe found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato.

Investigation of the role of AcTPR2 in kiwifruit and its response to Botrytis cinerea infection

BackgroundElucidation of the regulatory mechanism of kiwifruit response to gray mold disease caused by Botrytis cinerea can provide the basis for its molecular breeding to impart resistance against this disease. In this study, ‘Hongyang’ kiwifruit served as the experimental material; the TOPLESS/TOPLESS-RELATED (TPL/TPR) co-repressor gene AcTPR2 was cloned into a pTRV2 vector (AcTPR2-TRV) and the virus-induced gene silencing technique was used to establish the functions of the AcTPR2 gene in kiwifruit resistance to Botrytis cinerea.ResultsVirus-induced silencing of AcTPR2 enhanced the susceptibility of kiwifruit to Botrytis cinerea. Defensive enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and phenylalanine ammonia-lyase (PAL) and endogenous phytohormones such as indole acetic acid (IAA), gibberellin (GA3), abscisic acid (ABA), and salicylic acid (SA) were detected. Kiwifruit activated these enzymes and endogenous phytohormones in response to pathogen-induced stress and injury. The expression levels of the IAA signaling genes—AcNIT, AcARF1, and AcARF2—were higher in the AcTPR2-TRV treatment group than in the control. The IAA levels were higher and the rot phenotype was more severe in AcTPR2-TRV kiwifruits than that in the control. These results suggested that AcTPR2 downregulation promotes expression of IAA and IAA signaling genes and accelerates postharvest kiwifruit senescence. Further, Botrytis cinerea dramatically upregulated AcTPR2, indicating that AcTPR2 augments kiwifruit defense against pathogens by downregulating the IAA and IAA signaling genes.ConclusionsThe results of the present study could help clarify the regulatory mechanisms of disease resistance in kiwifruit and furnish genetic resources for molecular breeding of kiwifruit disease resistance.

Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice.

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

Integrated mRNA and Small RNA Sequencing for Analyzing Leaf Spot Pathogen Didymella segeticola and Its Host, Tea (Camellia sinensis), During Infection.

Leaf spot on tea plants (Camellia sinensis [L.] Kuntze), caused by the fungus Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola), negatively affects the productivity and quality of tea leaves in Guizhou Province, China. Although the genome sequence of D. segeticola has been published, no data on the transcriptome or microRNAs (miRNAs) of the pathogen or host during infection are available. Here, we report on the high-quality transcriptome and miRNA sequences of both D. segeticola and tea during infection, using the Illumina HiSeq 4000 or HiSeq 2500 platforms. Comprehensive expression profiling of the fungal pathogen and its host will provide a resource for future research into trait-specific genes of the pathogen and the host as well as on host-pathogen interactions and on disease resistance mechanisms.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BackgroundThe NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved.ResultsIn this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata.ConclusionProximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

An Observational Study to Collect and Assess Tissue Samples from Subjects with One of Three Neoplastic Conditions (ANSWer)

Background: Multiple studies have demonstrated that established human cancer cell lines are inadequate to model intra- and inter-patient tumor heterogeneity and resulting mechanisms of disease resistance and progression. Ex vivo drug sensitivity screening (DSS) on primary patient samples may provide a unique approach to overcome these limitations, unlocking insights into drug resistance and identify novel combination therapies that overcome resistance. Notable Labs has built an automated, flow-cytometry-based high-throughput DSS platform that enables testing hundreds of drugs and combinations on individual patient samples at scale. In addition, custom-built software facilitates data analysis and delivery of results within clinically actionable turnaround times.1 This technology platform is in use in the ANSWer study to obtain evidence for potential clinical utility of DSS in clinical practice and management of hematologic malignancies. Study Design and Methods: This is a prospective, multicenter, observational study with collection of de-identified biospecimens with matched clinical data from up to 1000 participants from clinical networks in the United States and Canada. Clinical information, demographics, and medical data relevant to cancer status are collected from all participants and their medical record at baseline (at study entry and time of baseline biospecimen collection), and subsequent visits per patient consent, for up to 1 year. The primary assessment is the establishment of a tumor registry with annotated clinical outcomes. Exploratory assessments include correlation of ex vivo functional testing results with clinical outcomes, as well as identification of potential biomarkers that correlate responses with genotype and/or phenotype. Inclusion Criteria: Provide written informed consent; Age ≥ 18 years, male or female, of any race; Suspected hematologic malignancy (any of the below), in need of starting an active anti-cancer therapy* Acute myelogenous leukemia (AML)a Multiple myeloma (MM) Myelodysplastic syndrome (MDS)a Lymphoma Acute lymphocytic leukemia (ALL) Chronic lymphocytic leukemia (CLL) Chronic myelogenous leukemia (CML) Myeloproliferative Neoplasm (MPN)a Other (upon review and approval by medical monitor) Intent to start anti-cancer therapy within 21 days of biospecimen collection; ≥ 7 days from last anti-cancer therapy; Any number of prior therapies Subject's cohort is currently opena *Supportive care agents including erythropoiesis-stimulating agents (ESAs) such as EPO, Procrit, Aranesp, etc; granulocyte colony stimulating factor (GCSF); hydroxyurea (Hydrea); and luspatercept (Reblozyl) are not considered anti-cancer therapy for this study aCohorts currently open and enrolling: AML, MDS, MPN Exclusion Criteria: Unwilling or unable to give consent; Disease is in remission; Subject's cohort is not open at the time of consent; Subject is restarting an ongoing treatment regimen after a dose interruption Statistical Methods: For the primary assessment, descriptive statistics will be used to summarize baseline patient characteristics, therapies, clinical outcomes, and collection of biospecimens. For exploratory analyses,hierarchical clustering using Euclidean distance metrics and Ward minimum variance will be used to identify patient clusters with distinctex vivodrug sensitivity patterns within a particular treatment cohort. The correlation between clinical response and drug sensitivity will be assessed using the area under the receiver-operator curve (AUROC) and bootstrapping to test for significance. A generalized estimation equation model will be used to identify associations between additional exploratory biomarkers, such as somatic mutations identified via NGS, andex vivosensitivity to various drug classes within specific treatment cohorts. 1Spinner M, et al. Ex Vivo Drug Screening Defines Novel Drug Sensitivity Patterns for Informing Personalized Therapy in Myeloid Neoplasms. Blood. 2020 June 23; 4(12):2768-2778. DOI: 10.1182/bloodadvances.2020001934. The ANSWer Study is currently enrolling at multiple sites across the US with plans to expand in the US and Canada: Figure Disclosures Wen: Notable Labs:Current Employment, Current equity holder in private company.Richardson:Notable Labs:Current Employment, Current equity holder in private company.Kita:Notable Labs:Current Employment, Current equity holder in private company.Tada:Notable Labs:Current Employment, Current equity holder in private company.

Evaluation of the potential SNPs for breeding selection of white spot syndrome virus resistance in Litopenaeus vannamei

White spot syndrome virus (WSSV) is a dangerous virus causing great damage to shrimp farming. Many genes related to disease resistance mechanisms have been identified and studied. In this study, we amplified and sequenced nine fragments of DNA harboring SNPs in the genes involved in WSSV resistance of white-legged shrimp, Litopenaeous vannamei. Allele frequencies at the SNP loci were recorded and calculated by SPSS statistical software (version 22) in the study groups: the disease shrimp (were infected with WSSV and died) and the resistance shrimp (were infected with WSSV but survived). Six SNPs (in AIF, ALF1, HAE, P53, Rab5B, and TRAF6 genes) were in accordance with Hardy–Weinberg Equilibrium (HWE) (p > 0.05) while three SNPs (in ALF2, BGB, and CAL) were not (p < 0.05). For AIF and ALF1 genes, the frequencies of GG and CC genotypes were significantly different between two groups and were associated with an decreased resistance with WSSV compared to the AA and TT genotypes (p = 0.021 and p = 0.017, respectively). The G and C alleles were associated with a decreased resistance with WSSV (p = 0.000 and p = 0.001, respectively). For HAE gene, the frequency of TT genotype was significantly different between two groups and was associated with a increased resistance with WSSV compared to the TC+CC genotype (OR = 68.750; 95% CI: 11.462–412.381; p = 0.000). For Rab5B gene, the frequency of CC genotype was significantly different between two groups and was associated with an increased resistance with WSSV compared to the TT genotype in all three tested models (p<0.05). The C allele was associated with an increased resistance with WSSV (OR = 3.974; 95% CI: 1.754–9.003; p = 0.001). The above evaluation results suggested that the potential SNPs of these AIF, ALF1, HAE, and Rab5B genes can be used as the molecular markers for breeding selection the resistance to white spot disease in white-legged shrimp L. vannamei.

Transcriptome analysis reveals immune pathways underlying resistance in the common carp Cyprinus carpio against the oomycete Aphanomyces invadans

Infection with Aphanomyces invadans is a serious fish disease with major global impacts. Despite affecting over 160 fish species, some of the species like the common carp Cyprinus carpio are resistant to A. invadans infection. In the present study, we investigated the transcriptomes of head kidney of common carp experimentally infected with A. invadans. In time course analysis, 5288 genes were found to be differentially expressed (DEGs), of which 731 were involved in 21 immune pathways. The analysis of immune-related DEGs suggested that efficient processing and presentation of A. invadans antigens, enhanced phagocytosis, recognition of pathogen-associated molecular patterns, and increased recruitment of leukocytes to the sites of infection contribute to resistance of common carp against A. invadans. Herein, we provide a systematic understanding of the disease resistance mechanisms in common carp at molecular level as a valuable resource for developing disease management strategies for this devastating fish-pathogenic oomycete.