DNA Methylation and RNA-Sequencing Analysis to Identify Genes Related to Spontaneous Leaf Spots in a Wheat Variety ‘Zhongkenuomai No.1’

Abstract

Greenish leaf variation has been reported widely as a trait of great interest in wheat for improving photosynthesis. Zhongkenuomai No.1 (ZKNM1), a mutant with recoverable leaf spots, was regarded as a suitable material for studying chlorophyll synthesis-related mechanisms. In this study, transcriptome and DNA methylation analyses were conducted in ZKNM1 leaves to determine the transcriptional regulatory mechanism of leaf spot development. Ultimately, 890 differentially expressed genes (DEGs) were discovered, with chlorophyll biosynthesis pathway genes downregulated and chlorophyll degradation pathway genes upregulated, possibly acting as a double block to chlorophyll accumulation. Among them, HEMA1s (Glutamyl-tRNA reductase family proteins) and PORAs (protochlorophyllide oxidoreductase A) were the most important controlled genes. Furthermore, a genome-wide methylation analysis indicates that a hypermethylated region is present 1690 bp upstream of the transcriptional start sites in spot tissues (SPs), and 131 DNA methylation-mediated DEGs were identified, one of which encoded a putative resistance gene (TraesCS1A02G009500) and was a hub gene in interaction network modules. In the sample groups with leaf spots (SPs), this gene may be involved in the photosynthetic processes. The findings indicated that dynamic variations in DNA methylation play key roles in gene regulation to govern leaf spot development.

Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and possibly influenced by cultivation

“…The few species of mostly agricultural use that show chloroplast methylation, such as tomato and rice, or the unicellular green alga Chlamydomonas (Muniandy et al., 2019 ; Niederhuth et al., 2016 ; Nishimura et al., 1999 ; Wang, Leister, & Kleine, 2020 ), typically have been analysed via methods that fall under the umbrella of whole genome bisulphite sequencing (WGBS; Muniandy et al., 2019 ; Nishimura et al., 1999 ). A recent method for non‐model organisms that captures methylation in CG and CHG sequence contexts is the MethylRAD method (Wang et al., 2015 ), which since has broadened methylome research (Dixon & Matz, 2020a , Dixon & Matz, 2020b : marine invertebrates and reef‐building coral; Jueterbock et al., 2020 : Seagrass; Saha et al., 2020 : differentiating embryonic stem cells; Scheschonk et al., 2022 : kelp; YanJun et al., 2021 : potato; Niu et al., 2022 : viviparous black rockfish; Xu et al., 2022 : leaf spots in wheat). These studies collectively highlight the versatility and effectiveness of the MethylRAD method in various biological research areas.…”