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

Abstract

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.

Identification and validation of coding and non-coding RNAs involved in high-temperature-mediated seed dormancy in common wheat

“…This indicates that a complex regulatory mechanism is involved in HT-mediated SD. The above differentially expressed mRNAs were mainly enriched in benzoxazinoid biosynthesis, starch and sucrose metabolism, and protein processing in the endoplasmic reticulum and in amino sugar, consistent with previous transcriptome data of dormancy ( Kato-Noguchi, 2008 ; Liew et al., 2020 ; Zhang et al., 2021 ). Interestingly, some pathways found in the present study, including nucleotide sugar metabolism and valine, leucine, and isoleucine biosynthesis, have not yet been reported to be associated with SD; these findings need to be validated in the future.…”

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat

“…A similar analysis on strong dormant AC Domain and weak dormant RL4452 showed that DEGs including wheat LONELY GUY (TaLOG), cis ZEATIN-O-GLUCOSYLTRANSFERASE (TacZOG), ALDEHYDE OXIDASE (TaAO), UBIQUITIN (TaRUB), and AUXIN RESPONSE FACTOR (TaARF) are involved in seed dormancy during the early stage of seed maturation [16]. Transcriptomic comparison of germination seeds and dormant seeds of the wheat variety MingXian169 revealed 3027 DEGs, and qRT-PCR confirmed that that the expressions of ASCORBATE PEROXIDASE (APX), MONODEHYDROASCORBATE REDUCTASE (MD-HAR), β-GLUCOSIDASE (GLU), and β-AMYLASE (AMY) are significantly upregulated in germination seeds [17].…”

“…There are thirty high-confidence genes in the QGp/Gi.sxau-6B interval according to the annotation of coding sequences (RefSeq v1.1) in the Chinese Spring genome database, five of which were highly expressed in germinated seeds but lowly expressed in dormant seeds based on published data [17]. Among these differentially expressed genes (DEGs), two genes TraesCS6B02G049100 and TraesCS6B02G049300 encoded histone H2B, two genes TraesCS6B02G049400 and TraesCS6B02G049500 encoded histone H2A, and the remain gene TraesCS6B02G050700 encoded carboxypeptidase (CP) (Figure 6).…”

Update on functional analysis of long non-coding RNAs in common crops

“…Nuclear lncRNAs interact with DNA, RNA, proteins, and other molecules to regulate chromosome structure and function, while also controlling gene transcription (cis- or trans-regulation). In contrast, cytoplasm-localized lncRNAs have post-transcriptional regulatory effects ( Zhang M. et al, 2021 ; Dietrich et al., 2015 ; Hu et al., 2023 ). The interaction between lncRNAs and proteins may be confirmed using various approaches, including pull-down assays, RNA-binding protein immunoprecipitation (RIP), cross-linking immunoprecipitation (CLIP), and chromatin isolation by RNA purification (ChIRP) ( Ferrè et al., 2016 ; Jiang et al., 2023 ).…”