Analysis of gene expression in early seed germination of rice: landscape and genetic regulation

Haoxuan Li,Guanjie Wang,Jianhua Zhang,Xiaozheng Li,Guanqun Wang

doi:10.1186/s12870-022-03458-3

Abstract

BackgroundSeed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. However, a specific genome-wide analysis of early seed germination in rice is still obscure.ResultsIn this study, the physiological characteristics of rice seed during seed germination are determined to define key points of early seed germination. Transcriptome analyses of early phase of seed germination provided deeper insight into the genetic regulation landscape. Many genes involved in starch-to-sucrose transition were differentially expressed, especially alpha-amylase 1b and beta-amylase 2, which were predominantly expressed. Differential exon usage (DEU) genes were identified, which were significantly enriched in the pathway of starch and sucrose metabolism, indicating that DEU events were critical for starch-to-sucrose transition at early seed germination. Transcription factors (TFs) were also dramatic expressed, including the abscisic acid (ABA) responsive gene, OsABI5, and gibberellic acid (GA) responsive genes, GAI. Moreover, GAI transactivated GA responsive gene, GAMYB in vivo, indicating a potential pathway involved in early seed germination process. In addition, CBL-interacting protein kinase (CIPK) genes, such as CIPK13, CIPK14 and CIPK17 were potentially interacted with other proteins, indicating its pivotal role at early seed germination.ConclusionTaken together, gene regulation of early seed germination in rice was complex and protein-to-gene or protein-to-protein interactions were indispensable.

Highlights

Seed germination is a crucial process, which determines the initiation of seed plant life cycle
Physiological characteristics of seed germination at the early stages To gain insight into the molecular mechanism of rice seed (Oryza sativa. japonica) germination initiation, we performed the seed germination experiment to find out the time of starting germination
Starch degraded into sucrose by amylase enzyme is important to support seeds germination

Summary

Introduction

Seed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. Phases from initially water uptake to radicle growing out of the covering seed layers was the most important stage in seed germination, thereafter, acquiring a comprehensive knowledge of this stage is necessary. Previous studies of proteomics on rice seeds germination were mainly focused on seeds germination time-course from the dry seeds to the formation of complete seedlings [16,17,18,19], whereas gene expression profile of seeds germinated in the most important stage compared with the water uptake stage is still obscure. Time point of seeds starting to germinate is essential for understanding the multi-regulations during seeds germination

Methods

Results

Conclusion