Dataset Information

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska.

ABSTRACT: BACKGROUND:Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield significantly and has also created problems in storage. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska collected over 10?years. Morphological features and ISSR-based DNA markers were used to study the morphogenetic diversity. RESULTS:Fungal colonies were morphologically diverse in shapes, aerial hyphae formation, colony, and sclerotia color. Marker analysis using 19 polymorphic ISSR markers showed polymorphic bands ranged from 15 to 28 with molecular weight of 100?bp to 3?kb. Polymorphic loci ranged from 43.26-92.88%. Nei genetic distance within the population ranged from 0.03-0.09 and Shannon diversity index varied from 0.24-0.28. AMOVA analysis based on ?PT values showed 87% variation within and 13% among the population with statistical significance (p

SUBMITTER: Das S

PROVIDER: S-EPMC7672822 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska.

Das Saurav S Plyler-Harveson T T Santra Dipak K DK Maharjan Bijesh B Nielson Kathy A KA Harveson Robert M RM

BMC microbiology 20201117 1

<h4>Background</h4>Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield significantly and has also created problems in storage. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska collected over 10 years. Morphological features and ISSR ...[more]

PMID: 33203383

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Project description:Background: Sugar beet is an important root crop, accounting for 30 % of the sugar production worldwide. The long growing season make sugar beets exposed to a range of plant pathogens for longer periods than most other crops. Here, contrasting sugar beet genotypes were used for transcriptome analysis to reveal differential responses and new defense genes to Rhizoctonia solani, a soilborn fungal pathogen. Results: After curation of primary RNA-sequencing reads, 16,768 genes deriving from 36 samples composed of two susceptible and two resistant sugar beet genotypes, three time-points (0, two and five days post inoculation), each in three replicates were subjected for analysis. Among the elevated 217 transcripts at 2 dpi, three resistance-like genes (Bv4_088600_cumk, Bv8u_204980_frqg, and Bv_44840_iifo) were activated. By employing edgeR package statistics, 660 genes were significantly different (false discovery rate < 0.05) between resistant and susceptible genotypes in their response to R. solani inoculation. A combination of eukaryotic orthologous group assignments and gene ontology enrichment analyses, revealed three Bet v I/Major latex protein homologous genes (Bv7_162510_pymu, Bv7_162520_etow, Bv_27270_xeas) in the resistant genotypes after five days of fungal challenge. Co-expression network analysis of differentially expressed sugar beet genes further identified a MYB46 transcription factor, a plant disease resistance response protein (DRR206) and a flavonoid o-methyltransferase protein. MYB46 has a key function in secondary cell wall formation and exist as a singleton in the sugar beet genome. The genome of R. solani is enriched in cell wall degrading enzyme encoding genes and it is anticipated that they represent important virulence factors. Compared to Arabidopsis thaliana, sugar beet has 2.4-fold more carbohydrate esterases and particularly large numbers (26-fold) of auxiliary activity encoding genes whose function in cell wall biosynthesis is largely unknown. Conclusions: Based on components identified in this sugar beet transcript data set we conclude that defense responses to R. solani are attributed to a wide range of gene categories but functional information is missing to a large extent. This calls for careful integration to avoid negative side effects to obtain optimal combinations of these traits in order to reach the long-term goal of improved resistance in sugar beet.

Project description:Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (F ST ), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

Dataset Information

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska.

Publications

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska.

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