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Exploiting DNA methylation in cassava under water deficit for crop improvement
Saturday, 2024/10/12 | 10:00:41

Jorge Luís Bandeira da Silva FilhoRosa Karla Nogueira PestanaWilson José da Silva JúniorMaurício Antônio Coelho FilhoClaudia Fortes FerreiraEder Jorge de OliveiraEderson Akio Kido

PLoS One; 2024 Feb 22; 19(2):e0296254. doi: 10.1371/journal.pone.0296254.

 

Abstract

DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.

 

See https://pubmed.ncbi.nlm.nih.gov/38386677/

 

Fig 4. Venn diagram using Manes identifiers (Manihot esculenta, Phytozome v.12.1) with differential methylation sites detected for BRS Formosa (bitter) and BRS Dourada (sweet) varieties in comparison to contrast with and without water deficit.

a) all identifiers detected with methylated sites (CCGG and CCNGG); b) methylated identifiers related to genes; c) Venn diagram using Manes identifiers (Mesculenta, Phytozome v.12.1) with hyper and hypomethylated sites (CCGG and CCNGG) in genes, detected in the contrast comparison with and without water deficit for the biiter variety BRS Formosa (FNC vs FST) and for the sweet BRS Dourada (DNC vs DST); FST (BRS Formosa, Stress Treatment); FNC (BRS Formosa, negative control); DST (BRS Dourada, Stress Treatment); DNC (BRS Dourada, negative control).

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