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Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance
Friday, 2024/09/27 | 08:37:45
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Camila Santiago Hohenfeld, Saulo Alves Santos de Oliveira, Claudia Fortes Ferreira, Victor Hugo Mello, Gabriel Rodrigues Alves Margarido, Adriana Rodrigues Passos, Eder Jorge de Oliveira Sci Rep.; 2024 May 8; 14(1):10587. doi: 10.1038/s41598-024-60847-4. AbstractCassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.
See https://pubmed.ncbi.nlm.nih.gov/38719851/
Figure 2: (A) Multidimensional scaling plot (MDSPlot) based on logFC (Fold Change) values generated by counting the reads of BRS Kiriris and BGM-1345 genotypes, inoculated with pathogens associated with root rot. (B) Mean-difference plot (MD-Plot) based on differential gene expression tests at each time-period for the contrast between BRS Kiriris × BGM-1345. Up-regulated indicates the genes of increased expression and Down-regulated indicates repressed genes in BRS Kiriris, Non-DE = not differentially expressed. (C) Venn diagram with differentially expressed transcripts (p-value < 0.05) of the interaction between cassava genotypes versus root rot for each of the treatments (Control, Initial time-period and Final time-period). Absolute numbers represent differentially expressed transcripts that are unique or common among pairs or among all treatments.
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