Comparative analysis of the transcriptomes of two rice subspecies during domestication

Hongbo Pang,Qingwen Yang,Yueying Li,Longkun Wu,Ze Wang,Xiaoming Zheng,Qiang Chen

doi:10.1038/s41598-021-83162-8

Abstract

Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

Highlights

It has been speculated that these gene regulatory regions may have evolved under positive selection pressure[23,24,25,26]
This study has the following conclusions: (1) we report that the two rice subspecies have 1357 different gene expression profiles; (2) we propose the relationship between the differentially expressed genes (DEGs) and the phenotypic differences, including grain shape, cold tolerance and nitrate-absorption; and (3) we speculate that nucleotide diversity in gene regulatory regions may associate with the phenotypic differences and play an important role in crop domestication
After filtering out low-quality reads and reads containing adaptor sequences (7% of all reads), we obtained approximately 4.52 billion clean reads (345.48 and 331.99 Gb for indica and japonica accessions, respectively) (Table S2). These clean reads were mapped to the reference japonica rice genome (Nipponbare; IRGSP v7.0), with at most two mismatches allowed for each read, while ignoring the reads that were mapped to more than two locations in the reference genome

Summary

Introduction

It has been speculated that these gene regulatory regions may have evolved under positive selection pressure[23,24,25,26]. We analyzed the transcriptomes in the young panicle of 26 indica and 25 japonica accessions using RNA- Seq and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. On this basis, we compared the transcriptomes of the two subspecies and identified 1357 differentially expressed genes (DEGs) between indica and japonica rice. This study has the following conclusions: (1) we report that the two rice subspecies have 1357 different gene expression profiles; (2) we propose the relationship between the DEGs and the phenotypic differences, including grain shape, cold tolerance and nitrate-absorption; and (3) we speculate that nucleotide diversity in gene regulatory regions may associate with the phenotypic differences and play an important role in crop domestication. The results of this study improve our understanding of the rice genome

Methods

Results

Conclusion