Dataset Information

Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination.

ABSTRACT: The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5'-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination.

SUBMITTER: He D

PROVIDER: S-EPMC4683037 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination.

He Dongli D Wang Qiong Q Wang Kun K Yang Pingfang P

PloS one 20151217 12

The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigat ...[more]

PMID: 26681181

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Project description:Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Project description:BackgroundImproving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions.ResultsThe analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039-15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662-690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected.ConclusionsThese results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

Dataset Information

Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination.

Publications

Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination.

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