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Transcriptome analysis reveals potential genes associated with plant height in rice

CAN CHEN#, RUI FENG#, ZONGQIONG ZHANG#, XIUZHONG XIA, BAOXUAN NONG, YU ZENG, HUI GUO, XINGHAI YANG*, DANTING LI*
Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
* Corresponding Authors: XINGHAI YANG. Email: ; DANTING LI. Email:

BIOCELL 2023, 47(2), 409-421. https://doi.org/10.32604/biocell.2023.023543

Received 30 April 2022; Accepted 24 September 2022; Issue published 18 November 2022

Abstract

Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs, of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction, ABC transportation, and steroid hormone biosynthesis. Among these metabolic pathways, LOC_Os05g43910 and LOC_Os01g35030 were auxin (IAA)-related genes, up-regulated in MUT and LOC_Os02g08500 (LEPTO1), LOC_Os11g04720, and LOC_Os12g04500 were cytokinin (CK)-related genes, down-regulated in MUT. The WGCNA identified four modules (light cyan, dark grey, grey, and pale turquoise) closely related to PH, and seven key genes were screened from these modules, of which two were up-regulated cell wall-related genes (LOC_Os01g26174 (OsWAK5), LOC_Os06g05050) in MUT, and one gibberellic acid (GA) gene (LOC_Os06g37364, OsKO2) was also up-regulated. These genes might be closely related to PH regulation. These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

Keywords

Rice; Plant height; Transcriptome; Weighted gene co-expression network analysis; Differentially expressed gene

Supplementary Material

Supplementary Material File

Cite This Article

CHEN, C., FENG, R., ZHANG, Z., XIA, X., NONG, B. et al. (2023). Transcriptome analysis reveals potential genes associated with plant height in rice. BIOCELL, 47(2), 409–421.



This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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