Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed.

Baosheng Huang,Changfeng Zhang,Zhaojian Song,Zhisong Wei,Xiangli Liu,Yuchi He,Liqi Tong,Yujie Zhang,Dongjie Chen,Lu Gan,Si Chen,Detian Cai,Xianhua Zhang,Yachun Zhang,Baohong Zhang

doi:10.1371/journal.pone.0242260

Abstract

Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.

Highlights

Rice (Oryza sativa L.) seed is the core of rice production, the “chip” of the rice industry
We focused on RNA integrity by omics analysis, to investigate the relationship between seed vigor and RNA damage in rice seeds
The results showed that the content of malondialdehyde, a product of peroxidation of lipids by reactive oxygen species (ROS), was significant higher in diploid rice seeds than that in tetraploid rice seeds, a response which was negatively correlated (r = -0.8927) with the activity of antioxidant enzymes

Summary

Introduction

Rice (Oryza sativa L.) seed is the core of rice production, the “chip” of the rice industry. Further elucidation of the delayed senescence mechanism in seeds is essential, as is improvement

Methods

Results

Discussion

Conclusion