DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Abstract

Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

Transcriptome Sequencing and Metabolome Analysis Reveals the Regulatory and Molecular Mechanisms of the Grain Filling Rate in Foxtail Millet (Setaria italica L.)

“…Foxtail millet grain filling progress is crucial for seed setting, grain weight, quality, and yield [39]. This process is highly sophisticated, involving the accumulation of carbohydrates and other nutrients by the developing endosperm to synthesize starch and enhance grain development [52].…”

“…Subsequently, clean reads were obtained by filtering out unqualified raw reads, based on Q20, Q30, and GC content criteria. The clean reads were trimmed with Trimmomatic (version 0.36) [41] while HISAT2 (version v2.0.5) [42] mapped them to the reference genome of foxtail millet [39]. Differential expression analysis of genes was performed using the DESeq package with BaseMean value estimation [43].…”

“…High-throughput sequencing technology and multi-omics analysis are among the means used to look for genes affecting grain filling. By comparing the differences in transcriptome- [9,36,37], metabolome- [38], and genome-wide DNA methylation in foxtail millet [39] at different grain filling stages, numerous potential regulators of grain filling and the accumulation of grain metabolites have been identified [35,39]. Furthermore, one paper has provided evidence of differences in the gene expressions and molecular mechanisms related to seed filling among foxtail millet cultivars with different panicle types in the North China summer sowing region [40].…”

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

“…This mutant resulted in reduced boron with thicker cell walls in Setaria ( Wang et al, 2021b ). DNA methylation studies and transcriptome analysis revealed the role of epigenetic modifications during grain filling ( Wang et al, 2021d ). Recently, RNA-seq analysis of two mutants siaux1-1 and siaux-1-2 was performed to identify auxin-responsive factors beneath C 4 root system architecture in shaping the root apical meristem ( Tang et al, 2022 ).…”

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

“…DNA methylation is an important and conserved epigenetic modification [18] that happens in CG, and CHG contexts (symmetrical), or in CHH contexts (asymmetrical) [19]. DNA methylation has been shown to influence a variety of leaf features, including growth [20], senescence [21], shape [22], and pigmentation [23,24].…”