Analysis of candidate genes expression associated with defense responses to root and collar rot disease caused by Phytophthora capsici in peppers Capsicum annuum

Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genome-wide association study

BACKGROUND

Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. This study aimed to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a panel consisting of 157 Capsicum spp. genotypes. Multi-locus genome wide association study (GWAS) was conducted using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Individual plants were separately inoculated with P. capsici isolates, 'PWB-185', 'PWB-186', and '6347', at the 4-8 leaf stage and were scored for disease symptoms up to 14-days post-inoculation. Disease scores were used to calculate disease parameters including disease severity index percentage, percent of resistant plants, area under disease progress curve, and estimated marginal means for each genotype.

RESULTS

Most of the genotypes displayed root rot symptoms, whereas five accessions were completely resistant to all the isolates and displayed no symptoms of infection. A total of 55,117 SNP markers derived from GBS were used to perform multi-locus GWAS which identified 330 significant SNP markers associated with disease resistance. Of these, 56 SNP markers distributed across all the 12 chromosomes were common across the isolates, indicating association with more durable resistance. Candidate genes including nucleotide-binding site leucine-rich repeat (NBS-LRR), systemic acquired resistance (SAR8.2), and receptor-like kinase (RLKs), were identified within 0.5 Mb of the associated markers.

CONCLUSIONS

Results will be used to improve resistance to Phytophthora root rot in chile pepper by the development of Kompetitive allele-specific markers (KASP®) for marker validation, genomewide selection, and marker-assisted breeding.

Transcriptome-based analysis of candidate gene markers associated with resistance mechanism to Phytophthora melonis that causes root and crown rot in pumpkin

Root and crown rot incited by an oomycete, Phytophthora melonis , causes significant yield losses in commercial pumpkin (Cucurbita pepo ) production worldwide. Currently, resistant cultivars and knowledge of molecular mechanism of C. pepo against P. melonis are scarce. Here, we analysed the quantitative gene expression changes of 10 candidate gene markers (bHLH87, ERF014, HSF, MYB, PR-1, WRKY21, CPI, POD, PSK, SGT ) in pumpkin roots and leaves at three time points (h post-inoculation, hpi) following inoculation with P. melonis in two resistant (Ghelyani and Tanbal), and two susceptible (Marmari and Khoreshti) varieties of pumpkin. Gene expression using quantitative real time PCR along a time course revealed the strongest transcriptomic response at 48 and 72hpi in resistant genotypes, 1.1-2.7-fold in roots and leaves, respectively, with a high significant correlation (r =0.857**-0.974**). We also found that CPI , PSK, SGT1 and POD act as a dual regulator that similarly modulate immunity not only against P. melonis , but also against other diseases such as early blight (Alternaria cucumerina) , powdery mildew (Podosphaera xanthii ), downy mildews (Pseudoperonospora cubensis ), and pathogenic plant nematodes (Meloidogyne javanica ). Furthermore, significantly higher activities of the ROS scavenging defence enzymes, catalase (1.6-fold increase) and peroxidase (6-fold increase) were observed in the roots of resistant cultivars at different hpi compared with non-inoculated controls. In addition, the biomass growth parameters including leaf and root length, stem and root diameter, root fresh weight and volume were significantly different among studied genotypes. Cumulatively, the transcriptome data provide novel insights into the response of pumpkins for improving pumpkin breeding to P. melonis .

Phytophthora capsici, 100 Years Later: Research Mile Markers from 1922 to 2022

In 1922, Phytophthora capsici was described by Leon Hatching Leonian as a new pathogen infecting pepper (Capsicum annuum), with disease symptoms of root rot, stem and fruit blight, seed rot, and plant wilting and death. Extensive research has been conducted on P. capsici over the last 100 years. This review succinctly describes the salient mile markers of research on P. capsici with current perspectives on the pathogen's distribution, economic importance, epidemiology, genetics and genomics, fungicide resistance, host susceptibility, pathogenicity mechanisms, and management.

Assessing genetic diversity and population structure of Iranian melons (Cucumis melo) collection using primer pair markers in association with resistance to Fusarium wilt

We evaluated genetic diversity and population structure of Iranian melons (Cucumis melo L.) using combinations of 35 primer pairs: 15 Simple-Sequence-Repeats (SSR); 10 Inter-Simple-Sequence-Repeats (ISSR); and 10 Sequence-related amplified polymorphism (SRAP) markers in association with resistance to melon Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (FOM ). Genetic similarity was determined by simple matching coefficient (SSM) and dendrogram by clustering-analysis with unweighted pair groups using arithmetic averages (UPGMA). By combining ISSR-SSR-SRAP markers, a high degree of variation among the melons was detected. The mean polymorphism information content (PIC), marker index (MI), effective-number of alleles (I), expected heterozygosity (H), and Nei's gene diversity parameters were 0.392, 0.979, 1.350, 0.551 and 0.225, respectively. According to MI, PIC, I, H, and Nei indices evaluation, ISSR6, ISSR9, SRAP3, SRAP5, SSR3 and SSR6 had the best performance in genetic diversity of the related melons population. The 35 primers yielded a total of 264 bands, of which 142 showed polymorphism. Clustering of genotypes based on resistance to Fusarium wilt, and comparison with grouping on SSR, SRAP and ISSR marker revealed a significant compliance between disease severity and molecular marker dendrograms. Thus, increasing the number of molecular markers for genetic diversity provides a powerful tool for future agricultural and conservation tasks.

Transcriptome-based analysis of resistance mechanisms to Bipolaris sorokiniana, a common wheat root-rot disease

In common root and crown rot (CRR), Bipolaris sorokiniana (Sace.) is one of the important in wheat, causing considerable yield losses globally. Sources of resistance can provide a feasible and effective method of control for plant disease management. However, knowledge on mechanisms of resistance is scarce. We screened 33 wheat genotypes against B. sorokiniana under greenhouse and field conditions. In addition, real-time quantitative PCR (qPCR) analysis using ten novel candidate gene markers, Cre3, EDS1, LTP5, PGIP, PR-1, PIEP1, TLP, UGT, Stb6 and PFT, was conducted on leaves and roots, along with changes in activity of antioxidant enzymes, peroxidase, catalase, β-1,3-glucanase, and phenolic content for their involvement in disease impact mechanisms. Lowest disease severity was in 'Alvand', followed by 'Baharan' and 'Bam' as resistant genotypes. Quantitative gene expression showed that, although the candidate defence genes were upregulated 1.24- to 3.5-fold in wheat roots and leaves inoculated with B. sorokiniana, they were highly regulated in resistant varieties 'Alvand', 'Mehregan' and 'Bam'. Cre3, a resistance gene to cereal cyst nematode Heterodera filipjevi, was regulated in cultivars resistant to B. sorokiniana. Similar results were obtained for Stb6, a gene resistant to Septoria tritici blotch, EDS1 resistant to powdery mildew, Blumeria graminis, and the genes PR-1 and UGT resistant to leaf rust, Puccinia triticina. Antioxidant enzyme activity also showed the highest increases in resistant genotypes. In conclusion, the T. aestivum-B. sorokiniana interaction in resistant wheat cultivars uses defence-related genes and enzymes that protect wheat towards sustainable development. Further such studies will shed light on simultaneous resistance to other diseases in wheat cultivars.

Biochemical defense mechanism associated with host-specific disease resistance pathways against Rhizoctonia solani AG3-PT potatoes canker disease

Screening for resistance in 40 potato genotypes to Rhizoctonia solani AG-3PT-stem-canker, antioxidant enzymes activity as well as total phenol compounds were documented. Rhizoctonia solani AG-3PT-stem-canker is one of the most devastating diseases that leads to severe economic losses in potatoes, Solanum tuberosum globally. Crop management and eugenic practices, especially the use of resistance can be effective in reducing the disease incidence. However, the information about potato-R. Solani interaction is still limited. This study explored screening for resistance in forty potato genotypes to R. solani, analyzing biomass growth parameters (BGPs), as well as antioxidant enzymes activity of which peroxidase/peroxide-reductases (POXs), superoxide dismutase (SOD), polyphenol oxidase (PPO), catalase (CAT), phenylalanine ammonia-lyase (PAL), β-1,3-glucanase (GLU) and total phenol compounds (TPCs) were taken into account. In addition, we analyzed up-regulation of two gene markers (PR-1 and Osmotin), using reverse transcription quantitative PCR (RT-qPCR). For which, the resistant 'Savalan', partially resistant 'Agria', partially susceptible 'Sagita' and susceptible 'Pashandi' were selected to explore the trails in their roots and leaves over the time courses of 1, 2 and 3-weeks post inoculation (wpi) following inoculation. Cluster analysis divided potatoes into four distinct groups, based on disease severity scales (0-100%) significance. The BGPs, shoot and root length, fresh and dry weight, and root volume were also significantly higher in infected potatoes compared to non-inoculated controls. Antioxidant enzymes activity also indicated the highest increased levels for POX (fourfold at 3wpi), CAT (1.5-fold at 3wpi), SOD (6.8-fold at 1wpi), and PAL (2.7-fold at 3wpi) in the resistant genotype, 'Savalan', whereas the highest activity was recorded in TPC (twofold at 1 wpi), PPO (threefold at 3wpi), and GLU (2.3-fold at 1wpi) in partially resistant genotypes. Although the defense-related enzymatic activities were sharply elevated in the resistant and partially resistant genotypes following inoculation, no significant correlations were between the activity trends of the related enzymes. The two related gene markers also showed comprehensive transcriptional responses up to 3.4-fold, predominantly in resistant genotypes. Surprisingly, the PR-1 gene marker, basically resistant to Wilting agent Verticillium dahlia was overexpressed in resistant 'Savalan' and 'Agria' against R. solani AG3-PT. Similar results were obtained on Osmotin gene marker resistant to late-blight P. infestans, and early-blight Alternaria solani that similarly modulates immunity against R. solani. Furthermore, there was a significant correlation between resistance, enzyme activity, and gene expression in the aforesaid cultivars. Studying the physiological metabolic pathways of antioxidant enzymes activity appears to be an important direction in research to elucidate resistance to R. solani in potatoes.

Enzyme activity and population genetic structure analysis in wheat associated with resistance to Bipolaris sorokiniana-common root rot diseases

Common root rot disease (CRR) caused by Bipolaris sorokiniana (Sacc.) (Pleosporaceae), is an important fungal disease of wheat, Triticum aestivum (Poaceae), causing considerable yield losses globally. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot diseases. Moreover, resistance to CCR is quantitative in nature, and thus the mechanism is poorly understood. To this aim, we analyzed the activities of defense-related enzymes; peroxidase (POX), superoxide dismutase (SOD), polyphenol oxidase (PPO), catalase (CAT), phenylalanine ammonia-lyase (PAL), β-1,3-glucanase (GLU) and chitinase (CHI), as well as total phenol content (TPC) to CRR on the three known resistant wheat 'Alvand' and 'Bam', 'Mehregan' at different time points (wpi) following CRR pathogen, B. sorokiniana inoculation. Of which, were selected out of 33 wheat cultivars previously screened for resistance to CRR. We also analyzed the genetic variability of the entire germplasm, 33 wheat cultivars using seven simple sequence repeat (SSR) primer pairs. The activity of antioxidant enzymes was increased in the related resistant genotypes. Of which, 'Bam' had the highest increase in PPO, and GLU activities, followed by 'Alvand' in SOD, PAL, and CHI significantly. Whereas, 'Mehregan' showed the highest level of TPC, POX, and CAT activities. In addition, five out of seven used SSR primers produced a total of 20 polymorphic bands, of which the number of alleles in each gene locus varied within 3-7 bands. The polymorphism information content (PIC) value also ranged from 0.44 to 0.81, with the mean of 0.65, Shannon Information Index (I) between 0.29 and 0.63 with an average of 0.47 per locus, and Nei's gene diversity (h) value varied from 0.16 to 0.44 with an average of 0.32. The average number of effective alleles was 1.52, ranging between 1.21 and 1.8. The gene locus Xgwm 140 showed the highest diversity in the population genetic structure, which explains the ability of the primers to resolve the assayed germplasm. Thus, resistance to CRR in wheat was mainly related to the enhancement of antioxidant enzymes, although the specific metabolic pathways require further study. This study presents new insights for understanding resistance mechanisms of the selected wheat cultivars to CRR, thus improving wheat yield in the future.

Identification of novel associations of candidate genes with resistance to Rhizoctonia solani AG-3PT in Solanum tuberosum stem canker

To develop an understanding mechanism to define responding of potatoes to R. solani, we analyzed the expression of ten novel candidate gene-markers using reverse-transcription-quantitative PCR (RT-qPCR) in resistant 'Savalan' and partially resistant 'Agria' in contrast to susceptible 'Sagita', and partially susceptible 'Pashandi'. In addition, oxidant-enzymatic-activity of catalase and superoxide-dismutase, as well as biomass-growth-parameters; shoot and root length, fresh and dry weight, and root volume were considered as complementary factors to the involving mechanism accordingly. Gene-markers up-regulated maximum up to 3.5-fold with the highest correlation, r = 0.939** following R. solani-inoculation, predominantly in resistant genotypes. Surprisingly, WRKY8-gene, basically resistant to late-blight-Phytophtora infestans was also up-regulated to 2.3-fold in resistant 'Savalan' followed by 'Agria'. Similar results with 3.1-fold were obtained on Osmotin-gene resistant to early-blight-Alternaria alternata. Enzymatic-activity of catalase with 1.6-fold and superoxide-dismutase, 6.8-fold also showed the highest level of activity in resistant genotypes, and had a high significant correlation, r = 773** and r = 0.881** with expression levels of related gene-markers respectively. Similarly, there were significant differences in biomass-growth-parameters, but with reductions in partially susceptible 'Sagita' and susceptible 'Pashandi'. Conclusively, S. tuberosum-R. solani interaction revealed that certain gene-markers can cover resistance to more than one disease simultaneously.

Mecanismos de defensa en plantas de Capsicum contra Phytophthora capsici

Phytophthora capsici es un oomiceto causante de la pudrición de raíz, tallo, frutos y tizón foliar en varias especies vegetales de importancia agrícola, principalmente en Solanáceas del género Capsicum como ají y pimiento. Este fitopatógeno cosmopolita posee mecanismos de ataque que favorecen la rápida infección, colonización y reproducción en huéspedes susceptibles. Contrariamente, estos procesos son retrasados o evitados fuertemente por genotipos resistentes, debido principalmente a sus mecanismos de defensa. En esas interacciones incompatibles, las plantas resistentes de Capsicum reconocen el oomiceto y rápidamente expresan múltiples genes que posteriormente señalizan moléculas, que permiten la acumulación de compuestos fenólicos, fitoalexinas y especies reactivas de oxígeno, la actividad de diferentes enzimas, que pueden permitir incluso la formación de barreras físicas. Esta revisión aborda, expone y discute los avances y el progreso de las investigaciones a lo largo de los ultimos veinte años, referente a los mecanismos de defensa estructurales, bioquimicos y moleculares que utilizan las plantas resistentes de Capsicum para defenderse de P. capsici. Palabras claves. ají, pimiento, pudrición de raíz y corona, tizón foliar, resistencia vegetal

Genetic diversity and biochemical analysis of Capsicum annuum (Bell pepper) in response to root and basal rot disease, Phytophthora capsici

This study analyzed the genetic variability and biochemical characteristics of edible and ornamental accessions of pepper, Capsicum annuum, in response to root and basal rot disease (RCR), caused by Phytophthora capsici, using resistance screening and genetic variability via Inter Simple Sequence Repeat marker (ISSR), bio-mass parameters, and enzymatic activity of Peroxidase or peroxide reductases (POX), Superoxide dismutase (SOD), Polyphenol oxidase (PPOs), Catalase (CAT), Phenylalanine ammonia-lyase (PAL), β-1,3-glucanase and phenolic content. The resistance in C. annuum '37ChilPPaleo', '19OrnP-PBI' and '23CherryPOrsh' and susceptibility in '2BP-PBI', '24BP-301' and '26BPRStarlet' accessions were confirmed. Nineteen out of 21 ISSR primers generated 185 polymorphic bands with a mean percentage band of 98.5 %, and an average number of bands of 9.9 per primer. Biomass parameters were significantly higher in resistant genotypes than the susceptible ones and non-inoculated controls. All the seven candidate enzymes were highly up-regulated in the resistant C. annuum accessions '19OrnP-PBI', '37ChillP-Paleo' and '23CherryP-Orsh' inoculated with P. capsici The mean level of enzyme activity varied from 1.5 to 5.6-fold higher in the resistant C. annuum, of which SOD was increased by 5.6 fold, followed by PAL 4.40 and PPO 3.75 fold in comparison to susceptible and non-inoculated controls. Overall, there was no significant correlation between resistance and genetic variability, and also between genetic variability and enzyme activity levels. However, there was a highly significant correlation between the resistance, bio-mass parameters and enzyme activity levels.