Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses.

Minsu Park,Dowhan Lee,Sang-Yoon Shin,Chanseok Shin,Yun-Shil Gho,Hongman Moon,Woochang Choi,Ki-Hong Jung,Jong-Seong Jeon

doi:10.3389/fpls.2021.727302

Minsu Park, Dowhan Lee + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2021.727302

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Abstract

Pre-harvest sprouting (PHS) is one of the primary problems associated with seed dormancy in rice (Oryza sativa L.). It causes yield loss and reduces grain quality under unpredictable humid conditions at the ripening stage, thus affecting the economic value of the rice crop. To resolve this issue, understanding the molecular mechanism underlying seed dormancy in rice is important. Recent studies have shown that seed dormancy is affected by a large number of genes associated with plant hormone regulation. However, understanding regarding the effect of heat stress on seed dormancy and plant hormones is limited. This study compared the transcriptome and small RNAome of the seed embryo and endosperm of two contrasting japonica rice accessions, PHS susceptible (with low seed dormancy) and PHS resistant (with high seed dormancy), at three different maturation stages. We found that 9,068 genes and 35 microRNAs (miRNAs) were differentially expressed in the embryo, whereas 360 genes were differentially expressed in the endosperm. Furthermore, we identified and verified the candidate genes associated with seed dormancy and heat stress-related responses in rice using quantitative real-time PCR. We newly discovered eight hormone-related genes, four heat shock protein-related genes, and two miRNAs potentially involved in PHS. These findings provide a strong foundation for understanding the dynamics of transcriptome and small RNAome of hormone- and heat stress-related genes, which affect PHS during seed maturation.

Highlights

Rice (Oryza sativa L.) is one of the essential crops and the staple food for approximately 50% of the global population (Wei et al, 2013)
No significant changes in hormone− and abiotic stress-related genes were observed in the both GJ45 and GJ60 (Figures 4D,E). These results suggest that indole-3-acetic acid (IAA)−, Abscisic acid (ABA)−, ethylene−, and heat stressrelated genes with differential expression between the embryos of Gopum and Jowoon are responsible for the difference in the Pre-harvest sprouting (PHS) rate between the two accessions
A comprehensive review of the previous studies and the results of the present study suggest that interaction between ABA and ABA-related genes and between ABA and heat shock proteins (HSPs) contributes to seed dormancy during seed maturation

Summary

Introduction

Rice (Oryza sativa L.) is one of the essential crops and the staple food for approximately 50% of the global population (Wei et al, 2013). Under excess moisture conditions during the period between seed maturation and harvest, the proper seed dormancy is broken, which causes PHS, an important issue that must be overcome to avoid the reduction in grain quality and yield (Gubler et al, 2005). Understanding the molecular basis of seed dormancy and maturation is crucial for controlling PHS. The Osbhlh mutants showed delayed seed germination and up-regulated OsAAO3 expression (Chen et al, 2018). The overexpression of the F-box gene, OsFbx352, improves the germination rate of seeds when treated with ABA, and decreases the expression of ABA biosynthesis-related genes (OsNced and OsNced3) (Frey et al, 2012; Song et al, 2012)

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