Fusarium graminearum microRNA-like RNAs and their interactions with wheat genome: a much-needed study

Kharbikar, Lalit L.; Shanware, Arti; Saharan, M. S.; Nandanwar, Shweta K.; Sivalingam, P. N.; Gurjar, Malkhan Singh; Aggarwal, Rashmi

doi:10.1007/s42360-019-00139-4

“…Therefore, developing FHB resistance in the locally grown wheat cultivars is of great importance and a perfect solution for controlling this disease. However, in many crops including wheat, pathogen resistance is governed by the small RNA (sRNA)-regulated epigenetic expression of several genes in RNAi pathways (Kharbikar et al 2019). Epigenetic changes in response to endogenous and external stimuli play a de nitive role in the adaptation of organisms to adverse environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

An in – silico perspective on the role of methylation-related genes in wheat – Fuarium graminearum interaction

Kharbikar

¹

,

Shanware

²

,

Nandanwar

³

et al. 2022

Preprint

Self Cite

0

View full text Add to dashboard Cite

Wheat (Triticum aestivum L.), a most important crop among the cereals, accounts for over 20% of the total calories and protein available in human food. However, Fusarium graminearum, a devastating Fusarium head blight (FHB) pathogen of wheat, poses a greater threat to quality wheat grain production as it produces obnoxious mycotoxins. Presently, FHB is a minor disease in India but can cause significant yield and quality losses if rain occurs during mid-anthesis. In plants, epigenetics including DNA methylation and sRNA accumulation regulates gene expression and plays a definitive role in the adaptation to adverse environmental conditions. In a previous study response of wheat to F. graminearum was investigated through transcriptome analysis of lines differing for 2DL FHB resistance QTLs. However, a comprehensive analysis of methylation-related genes in response to pathogen was not performed in that study or any other studies. We re-analyzed the RNA-Seq data of said study to reveal the roles of methylation-related genes in response to F. graminearum. Sixteen methylation-related genes were down-regulated in a susceptible line, 2-2890 (pedigree of line). GO associated these genes with L-methionine salvage from methylthioadenosine and S-adenosylmethionine and steroid biosynthesis (p-value 0.001). Co-expression analysis of this NIL with methionine S-methyl-transferase gene (MSM; TraesCS1A02G013800) resulted in 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR; TraesCS5A02G269300). HMGCR was negatively correlated (-1.00) with genes encoding pathogenesis-related and detoxification proteins and xylanase inhibitors. GO associated these genes with methionine S-methyl transferase (p-value 0.001). Expression of HMGCR was higher (Log2 levels from 3.25 to 4.00) in pathogen inoculated compared to MSM (Log2 levels from 1.25 to 3.25) in mock-inoculated samples. 43 genes were down-regulated by miR9678. These genes are associated with responses to biotic stimulus and glucan endo-1,4-beta-glucanase in GO.

show abstract

“…However, few moderately resistant genotypes including AKDW 2997-16, DBW 62, PBW 396, PDW 311, UAS 415, UP 2747, UP 2798, VL 926, VL 829 and WH 1021 could be identi ed. As very limited sources of full resistance to FHB, including the Chinese cultivars Sumai 3 and Frontana, are available the control of this disease is challenging (Kharbikar et al 2019). This is because these sources may not be available to every wheat-growing country in the world due to weak material transfer agreements (MTA).…”

mentioning

confidence: 99%

“…Therefore, developing FHB resistance in the locally grown wheat cultivars is of great importance and a perfect solution for controlling this disease. However, in many crops including wheat, pathogen resistance is governed by the small RNA (sRNA)-regulated epigenetic expression of several genes in RNAi pathways (Kharbikar et al 2019).…”

mentioning

confidence: 99%

Role of methylation-related genes and microRNA revealed from RNA-Seq study of FHB susceptible hexaploid wheat NIL in response to pathogen stress

Kharbikar

¹

,

Shanware

²

,

Nandanwar

³

et al. 2021

Preprint

Self Cite

0

View full text Add to dashboard Cite

Wheat (Triticum aestivum L.), a most important crop among the cereals, accounts for over 20% of the total calories and protein available in human food. However, Fusarium graminearum, a devastating Fusarium head blight (FHB) pathogen of wheat, poses a greater threat to quality wheat grain production as it produces obnoxious mycotoxins. Presently, FHB is a minor disease in India but can cause significant yield and quality losses if rain occurs during mid-anthesis. In plants, epigenetics including DNA methylation and sRNA accumulation regulates gene expression and plays a definitive role in the adaptation to adverse environmental conditions. In a previous study response of wheat to F. graminearum was investigated through transcriptome analysis of lines differing for 2DL FHB resistance QTLs. However, a comprehensive analysis of methylation-related genes in response to pathogen was not performed in that study or any other studies. We re-analyzed the RNA-Seq data of said study to reveal the roles of methylation-related genes in response to F. graminearum. Sixteen methylation-related genes were down-regulated in a susceptible line, 2-2890 (pedigree of line). GO associated these genes with L-methionine salvage from methylthioadenosine and S-adenosylmethionine and steroid biosynthesis (p-value 0.001). Co-expression analysis of this NIL with methionine S-methyl-transferase gene (MSM; TraesCS1A02G013800) resulted in 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR; TraesCS5A02G269300). HMGCR was negatively correlated (-1.00) with genes encoding pathogenesis-related and detoxification proteins and xylanase inhibitors. GO associated these genes with methionine S-methyl transferase (p-value 0.001). Expression of HMGCR was higher (Log2 levels from 3.25 to 4.00) in pathogen inoculated compared to MSM (Log2 levels from 1.25 to 3.25) in mock-inoculated samples. 43 genes were down-regulated by miR9678. These genes are associated with responses to biotic stimulus and glucan endo-1,4-beta-glucanase in GO.

show abstract