scholarly journals Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11135
Author(s):  
Gina A. Garzón-Martínez ◽  
Francy L. García-Arias ◽  
Felix E. Enciso-Rodríguez ◽  
Mauricio Soto-Suárez ◽  
Carolina González ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Crop Improvement ◽  
Defense Responses ◽  
Economic Losses ◽  
Marker Genes ◽  
Physalis Peruviana ◽  
Cape Gooseberry

Vascular wilt, caused by the pathogen Fusarium oxysporum f. sp. physali (Foph), is a major disease of cape gooseberry (Physalis peruviana L.) in Andean countries. Despite the economic losses caused by this disease, there are few studies related to molecular mechanisms in the P. peruviana—Foph pathosystem as a useful tool for crop improvement. This study evaluates eight candidate genes associated with this pathosystem, using real-time quantitative PCR (RT-qPCR). The genes were identified and selected from 1,653 differentially expressed genes (DEGs) derived from RNA-Seq analysis and from a previous genome-wide association study (GWAS) of this plant-pathogen interaction. Based on the RT-qPCR analysis, the tubuline (TUB) reference gene was selected for its highly stable expression in cape gooseberry. The RT-qPCR validation of the candidate genes revealed the biological variation in their expression according to their known biological function. Three genes related to the first line of resistance/defense responses were highly expressed earlier during infection in a susceptible genotype, while three others were overexpressed later, mostly in the tolerant genotype. These genes are mainly involved in signaling pathways after pathogen recognition, mediated by hormones such as ethylene and salicylic acid. This study provided the first insight to uncover the molecular mechanism from the P. peruviana—Foph pathosystem. The genes validated here have important implications in the disease progress and allow a better understanding of the defense response in cape gooseberry at the molecular level. Derived molecular markers from these genes could facilitate the identification of tolerant/susceptible genotypes for use in breeding schemes.

scholarly journals Yield and physicochemical quality of Physalis peruviana L. fruit related to the resistance response against Fusarium oxysporum f. sp. physali

2019 ◽  
Vol 37 (2) ◽  
pp. 120-128
Author(s):  
Franklin Mayorga-Cubillos ◽  
Jorge Argüelles-Cárdenas ◽  
Edwin Rodríguez-Velásquez ◽  
Carolina González-Almario ◽  
Claudia Ariza-Nieto ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Crop Improvement ◽  
Physicochemical Characterization ◽  
Principal Component ◽  
Differential Resistance ◽  
Resistance Response ◽  
Physalis Peruviana ◽  
Fruit Cracking ◽  
Medicinal Value ◽  
Cape Gooseberry

Cape gooseberry (Physalis peruviana L.) is a fruit of great interest, due to its high nutritional and potential medicinal value. Vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. Physali (Foph) is responsible for crop losses of up to 100% which makes necessary to identify resistant cultivars. To contribute to crop improvement processes, a physicochemical characterization was performed on fruits of 33 cape gooseberry genotypes using 18 quantitative descriptors. The genotypes were planted in the field under high and no pressure of Foph. The Student’s t test detected statistically significant differences (P<0.05) between the two conditions for yield, fruit cracking (%) and fruit juice pH. The principal component analysis explained in five factors 84.96% of the total variance, in which the fruit physical variables were the major contributor to the first component (41.65%). Cluster analysis grouped the genotypes under high and no pressure in seven and eight clusters, respectively. Two contrasting genotypesshowing differential resistance response to the pathogen wereanalyzed for fruit antioxidant capacity, in which DPPH and ORAC methods presented significant differences (P<0.05) between the two genotypes with greater antioxidant activity in the susceptible material.

scholarly journals Hyperspectral response of cape gooseberry (Physalis peruviana L.) plants inoculated with Fusarium oxysporum f. sp. physali for vascular wilt detection

2020 ◽  
Vol 14 (3) ◽  
pp. 301-313
Author(s):  
Cristhian Giraldo-Betancourt ◽  
Edisson Andrés Velandia-Sánchez ◽  
Gerhard Fischer ◽  
Sandra Gómez-Caro ◽  
Luís Joel Martínez
Keyword(s):  
Fusarium Oxysporum ◽  
Spectral Response ◽  
Visible Spectrum ◽  
Economic Losses ◽  
Vascular Wilt ◽  
Physalis Peruviana ◽  
Red Edge ◽  
Progress Curve ◽  
Simple Ratio ◽  
Cape Gooseberry

This study used greenhouse conditions to determine the hyperspectral responses of cape gooseberry (Physalis peruviana L.) plants inoculated with different Fusarium oxysporum f. sp. physali densities because the causal agent of vascular wilt generates great economic losses for farmers. A completely randomized design with four replicates was established. The evaluated treatments were inoculum densities 0.0, 1.0·103 and 1.0·106 conidia/mL of the pathogen. The inoculation was done with immersion of roots in conidia suspensions. The spectral response was directly measured on the plant leaves with a spectroradiometer. Non-invasive detection in the P. peruviana - F. oxysporum pathosystem with reflectance values was used with different spectral indices related to the visible and Red Edge, which were calculated and correlated with the disease variables. The treatments showed significant differences in the visible spectrum starting 14 days after inoculation with higher reflectance values. The chlorophyll index at the red edge (ChRE), the modified chlorophyll absorption index (MCARI), the simple ratio index (SR) and the Zarco & Miller index (ZM) showed highly significant correlations with the area under the disease progress curve for leaves (AUDPCL), leaf area and fresh weight of the aerial part of the plants. This study showed the potential of spectral patterns for the detection and study of Fusarium wilt in P. peruviana.

scholarly journals The Novel Cerato-Platanin-Like Protein FocCP1 from Fusarium oxysporum Triggers an Immune Response in Plants

2019 ◽  
Vol 20 (11) ◽  
pp. 2849 ◽  
Author(s):  
Songwei Li ◽  
Yijie Dong ◽  
Lin Li ◽  
Yi Zhang ◽  
Xiufen Yang ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Pseudomonas Syringae ◽  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Defense Responses ◽  
Economic Losses ◽  
Seedling Resistance ◽  
Ros Formation ◽  
Serious Disease ◽  
Banana Wilt

Panama disease, or Fusarium wilt, the most serious disease in banana cultivation, is caused by Fusarium oxysporum f. sp. cubense (FOC) and has led to great economic losses worldwide. One effective way to combat this disease is by enhancing host plant resistance. The cerato-platanin protein (CPP) family is a group of small secreted cysteine-rich proteins in filamentous fungi. CPPs as elicitors can trigger the immune system resulting in defense responses in plants. In this study, we characterized a novel cerato-platanin-like protein in the secretome of Fusarium oxysporum f. sp. cubense race 4 (FOC4), named FocCP1. In tobacco, the purified recombinant FocCP1 protein caused accumulation of reactive oxygen species (ROS), formation of necrotic reaction, deposition of callose, expression of defense-related genes, and accumulation of salicylic acid (SA) and jasmonic acid (JA) in tobacco. These results indicated that FocCP1 triggered a hypersensitive response (HR) and systemic acquired resistance (SAR) in tobacco. Furthermore, FocCP1 enhanced resistance tobacco mosaic virus (TMV) disease and Pseudomonas syringae pv. tabaci 6605 (Pst. 6605) infection in tobacco and improved banana seedling resistance to FOC4. All results provide the possibility of further research on immune mechanisms of plant and pathogen interactions, and lay a foundation for a new biological strategy of banana wilt control in the future.

scholarly journals Transcriptome analysis reveals ethylene-mediated defense responses to Fusarium oxysporum f. sp. cucumerinum infection in Cucumis sativus

2020 ◽  
Author(s):  
Jingping Dong ◽  
Yuean Wang ◽  
Qianqian Xian ◽  
Xuehao Chen ◽  
Jun Xu
Keyword(s):  
Fusarium Oxysporum ◽  
Cucumis Sativus ◽  
Fusarium Wilt ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Severe Disease ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Positive Role

Abstract Background: Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is a severe disease affecting cucumber (Cucumis sativus L.) production worldwide, but the molecular mechanisms underlying Fusarium wilt resistance in cucumber remain unknown. To gain an improved understanding of the defense mechanisms elicited in response to Foc inoculation, RNA sequencing-based transcriptomic profiling of responses of the Fusarium wilt-resistant cucumber line ‘Rijiecheng’ at 0, 24, 48, 96, and 192 h after Foc inoculation was performed.Results: We identified 4116 genes that were differentially expressed between 0 h and other time points after inoculation. All ethylene-related and pathogenesis-related genes from among the differentially expressed genes were filtered out. Real-time PCR analysis showed that ethylene-related genes were induced in response to Foc infection. Importantly, after Foc infection and exogenous application of ethephon, a donor of ethylene, these genes were highly expressed. In response to exogenous ethephon treatment in conjunction with Foc inoculation, the infection resistance of cucumber seedlings was enhanced and endogenous ethylene biosynthesis increased dramatically. Conclusion: Collectively, ethylene signaling pathways play a positive role in regulating the defense response of cucumber to Foc infection. The results provide insight into the cucumber Fusarium wilt defense mechanisms and provide valuable information for breeding new cucumber cultivars with enhanced Fusarium wilt tolerance.

scholarly journals Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11707
Author(s):  
Yinchao Zhang ◽  
Peng Liu ◽  
Chen Wang ◽  
Na Zhang ◽  
Yuxiao Zhu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Seed Germination ◽  
Association Study ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Chilling Stress ◽  
Nucleotide Polymorphisms ◽  
Plant Tolerance ◽  
Multiple Traits

As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 ×  10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.

scholarly journals Differential Response of Tomato Plants to the Application of Three Trichoderma Species When Evaluating the Control of Pseudomonas syringae Populations

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 626 ◽  
Author(s):  
María E. Morán-Diez ◽  
Eduardo Tranque ◽  
Wagner Bettiol ◽  
Enrique Monte ◽  
Rosa Hermosa
Keyword(s):  
Pseudomonas Syringae ◽  
Molecular Mechanisms ◽  
Defense Responses ◽  
Marker Genes ◽  
Post Inoculation ◽  
Trichoderma Spp ◽  
Bacterial Populations ◽  
Oxidase Gene ◽  
Trichoderma Species ◽  
Tomato Plants

Trichoderma species are well known biocontrol agents that are able to induce responses in the host plants against an array of abiotic and biotic stresses. Here, we investigate, when applied to tomato seeds, the potential of Trichoderma strains belonging to three different species, T. parareesei T6, T. asperellum T25, and T. harzianum T34, to control the fully pathogenic strain Pseudomonas syringae pv. tomato (Pst) DC3000, able to produce the coronatine (COR) toxin, and the COR-deficient strain Pst DC3118 in tomato plants, and the molecular mechanisms by which the plant can modulate its systemic defense. Four-week old tomato plants, seed-inoculated, or not, with a Trichoderma strain, were infected, or not, with a Pst strain, and the changes in the expression of nine marker genes representative of salicylic acid (SA) (ICS1 and PAL5) and jasmonic acid (JA) (TomLoxC) biosynthesis, SA- (PR1b1), JA- (PINII and MYC2) and JA/Ethylene (ET)-dependent (ERF-A2) defense pathways, as well as the abscisic acid (ABA)-responsive gene AREB2 and the respiratory burst oxidase gene LERBOH1, were analyzed at 72 hours post-inoculation (hpi) with the bacteria. The significant increase obtained for bacterial population sizes in the leaves, disease index, and the upregulation of tomato genes related to SA, JA, ET and ABA in plants inoculated with Pst DC3000 compared with those obtained with Pst DC3118, confirmed the COR role as a virulence factor, and showed that both Pst and COR synergistically activate the JA- and SA-signaling defense responses, at least at 72 hpi. The three Trichoderma strains tested reduced the DC3118 levels to different extents and were able to control disease symptoms at the same rate. However, a minor protection (9.4%) against DC3000 was only achieved with T. asperellum T25. The gene deregulation detected in Trichoderma-treated plus Pst-inoculated tomato plants illustrates the complex system of a phytohormone-mediated signaling network that is affected by the pathogen and Trichoderma applications but also by their interaction. The expression changes for all nine genes analyzed, excepting LERBOH1, as well as the bacterial populations in the leaves were significantly affected by the interaction. Our results show that Trichoderma spp. are not adequate to control the disease caused by fully pathogenic Pst strains in tomato plants.

scholarly journals Identification of Genes Conferring Plant Salt Tolerance using GWAS: Current Success and Perspectives

2020 ◽  
Vol 61 (8) ◽  
pp. 1419-1426
Author(s):  
Bo Li
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Crop Improvement ◽  
Genome Wide Association ◽  
The Past ◽  
Genome Wide ◽  
Key Genes ◽  
Plant Salt Tolerance

Abstract An understanding of the molecular mechanisms that underlie plant salt tolerance is important for both economic and scientific interests. Genome-wide association study (GWAS) is a promising approach to pinpoint genes that confer plant salt tolerance. With the advancement of supporting technology and methodology, GWAS has enabled the discovery of genes that play central roles in regulating plant salt tolerance in the past decade. Here, I highlight recent successful GWAS work in unveiling the molecular factors underlying plant salt tolerance and discuss the concerns and opportunities in conducting such experiments. It is anticipated that GWAS will be increasingly successful in the identification of key genes that are useful for crop improvement.

scholarly journals Identification of novel variants and candidate genes associated with porcine bone mineral density using genome-wide association study

2020 ◽  
Vol 98 (4) ◽  
Author(s):  
Jiuhong-H Nan ◽  
Lilin-L Yin ◽  
Zhenshuang-S Tang ◽  
Tao Xiang ◽  
Guanjun-J Ma ◽  
...  
Keyword(s):  
Bone Mineral Density ◽  
Association Study ◽  
Candidate Genes ◽  
Bone Mineral ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Economic Losses ◽  
Mineral Density ◽  
Genome Wide ◽  
Leg Weakness

Abstract Pig leg weakness not only causes huge economic losses for producers but also affects animal welfare. However, genes with large effects on pig leg weakness have not been identified and suitable methods to study porcine leg weakness are urgently needed. Bone mineral density (BMD) is an important indicator for determining leg soundness in pigs. Increasing pig BMD is likely to improve pig leg soundness. In this study, porcine BMD was measured using an ultrasound bone densitometer in a population with 212 Danish Landrace pigs and 537 Danish Yorkshires. After genotyping all the individuals using GeneSeek Porcine 50K SNP chip, genetic parameter estimation was performed to evaluate the heritability of BMD. Genome-wide association study and haplotype analysis were also performed to identify the variants and candidate genes associated with porcine BMD. The results showed that the heritability of BMD was 0.21 in Landrace and 0.31 in Yorkshire. Five single-nucleotide polymorphisms on chromosome 6 identified were associated with porcine BMD at suggestive significance level. Two candidate quantitative trait loci (74.47 to 75.33 Mb; 80.20 to 83.83 Mb) and three potential candidate genes (ZBTB40, CNR2, and Lin28a) of porcine BMD were detected in this study.

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