Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice

Abstract

Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant–pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5′ end, and a non-conserved 3′ end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.

Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds

“…A genomic view of lncRNAs in rice seed revealed that lncRNAs undergo extensive alternative splicing during the transition from milk seed to mature embryo and endosperm, and lncRNAs could maintain more exons in embryos [57]. Alternative splicing forms of a rice lncRNA LNC_037529 were also identified in artificial aging seed [58]. These results suggest that the alternative splicing of lncRNA is widely present in metabolic processes.…”

Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage

“…LncRNAs participate in important age-related signaling pathways via regulation the expression of target genes in cis or trans modes 20 . A large number of differentially expressed lncRNAs were identified, which target genes were coding proteins involved in age-related signaling pathways, like enzymes associated with cell wall degradation, lipid peroxidation, and secondary metabolism 21 . Some DE-lncRNAs, such as lncRNAs MSTRG.31014.21 and MSTRG.31014.36, which are possibly involved in flag leaf senescence of rice could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) 22 .…”

Full-Length Transcriptome Sequencing Reveals the Molecular Mechanism of Metasequoia glyptostroboides Seed Responding to Aging

“…Wang et al identified that the transcription factor bZIP23 bound to the genetic factor PER1A of peroxidase in rice through metabolome and transcriptome technologies, and was involved in the clearance of reactive oxygen species during seed aging [11]. Zhang et al performed strand-specific RNA sequencing on rice embryonics of fresh-dried seeds (96% germination percentage) and aged seed samples (50% germination percentage; aged for 6 days at 43 • C and 85% relative humidity) and detected four upregulated lncRNAs that predominantly regulated target genes involved in base repair, either in cis or trans -regulated target genes [12]. Gu et al conducted an integrated analysis of proteomics and genomics on 20 different rapeseed varieties with varying oil contents, identifying 165 differentially expressed proteins (DEPs), and 31 unique genes showed significant differences in the germination process between high-and low-oil-content seeds, with 13 of these genes potentially being related to seed germination vigor [13].…”