RNA-seq and phytohormone analysis reveals the culm color variation of Bambusa oldhamii Munro

PeerJ. 2022 Jan 13;10:e12796. doi: 10.7717/peerj.12796. eCollection 2022.

Abstract

Background: The clumping bamboo Bambusa oldhamii Munro, known as "green bamboo", is famous for its edible bamboo shoots and fast-growing timber. The green and yellow striped-culm B. oldhamii variety, named B. oldhamii f. revoluta W.T. Lin & J. Y. Lin, is an attractive system for researching the culm color variation of B. oldhamii.

Methods: Millions of clean reads were generated and assembled into 604,900 transcripts, and 383,278 unigenes were acquired with RNA-seq technology. The quantification of ABA, IAA, JA, GA1, GA3, GA4, and GA7 was performed using HPLC-MS/MS platforms.

Results: Differential expression analysis showed that 449 unigenes were differentially expressed genes (DEGs), among which 190 DEGs were downregulated and 259 DEGs were upregulated in B. oldhamii f. revoluta. Phytohormone contents, especially GA1 and GA7, were higher in B. oldhamii. Approximately 21 transcription factors (TFs) were differentially expressed between the two groups: the bZIP, MYB, and NF-YA transcription factor families had the most DEGs, indicating that those TFs play important roles in B. oldhamii culm color variation. RNA-seq data were confirmed by quantitative RT-PCR analysis of the selected genes; moreover, phytohormone contents, especially those of ABA, GA1 and GA7, were differentially accumulated between the groups. Our study provides a basal gene expression and phytohormone analysis of B. oldhamii culm color variation, which could provide a solid fundamental theory for investigating bamboo culm color variation.

Keywords: ABA; Bambusa oldhamii; Culm color variation; GA1; GA7; HY5; MYB; Phytohormone; RNA-seq; Transcription factors.

Associated data

  • figshare/10.6084/m9.figshare.16912324.v3

Grant support

This work was financially supported by the Zhejiang Academy of Agricultural Sciences Youth Training Project (No. 2020R26R08E01), the Zhejiang Science and the Technology Major Program on Agricultural New Variety Breeding (No. 2021C02070-4), and the Wenzhou Agricultural New Variety Breeding Cooperation Project (No. 2019ZX004-2). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.