Regulatory Network of Preharvest Sprouting Resistance Revealed by Integrative Analysis of mRNA, Noncoding RNA, and DNA Methylation in Wheat

Preharvest
sprouting (PHS) of grain occurs universally and sharply
decreases grain quality and yield, but the mechanism remains unclear.
MingXian169, a breeding inducer wheat for stripe rust, is widely used
in the Huanghuai wheat-producing region, China. In this study, we
found that MingXian169 could be considered an ideal material for PHS
research because of its high PHS resistance. To further analyze the
network of PHS, transcriptome sequencing of mRNA, noncoding RNA (ncRNA),
and DNA methylome data were used to comparison germination seeds (GS)
and dormant seeds (DS); 3027, 1516, and 22 genes and 95 103
methylation regions were identified as differentially expressed mRNA,
DE-microRNAs (DE-miRNA), DE-long noncoding RNAs (DE-lncRNA), and differentially
methylated regions (DMRs). Pathway enrichment tests highlighted plant
hormone biosynthesis and signal transduction, glutathione–ascorbate
metabolism, and starch and sucrose metabolism processes related to
PHS mechanisms. Further analysis demonstrated that long noncoding
RNA, miRNA, and DNA methylation played critical roles in transcriptional
regulation of critical pathways during PHS by modifying and interacting
with target genes. Quantitative real-time polymerase chain reaction
(PCR) analyses of mRNA and miRNA confirmed the sequencing results.
In the phytohormone content assay, abscisic acid (ABA) and jasmonic
acid (JA) increased significantly in DS, and GA19 increased in GS.
The ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR),
and β-d-glucosidase (BGLU) enzyme activities and the
substance content of glutathione and sucrose were significantly higher
in GS than in DS, implying that they were responsible for increasing
PHS in MingXian169. Our results provide new insights into wheat PHS
resistance at mRNA, ncRNA, and DNA methylation levels, with suggestions
for crop breeding and production.