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Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA

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Abstract

Key message

Cold-tolerant QTL qCSS12-regulated 14 hub genes are involved in the chloroplastic biological processes and in the protein synthesis and degradation processes in japonica rice.

Abstract

Low temperature is a main constraint factor for rice growth and production. To better understand the regulatory mechanisms underlying the cold tolerance phenotype in rice, here, we selected a cold-sensitive nearly isogenic line (NIL) NIL(qcss12) as materials to identify hub genes that are mediated by the cold-tolerant locus qCSS12 through weighted gene co-expression network analysis (WGCNA). Fourteen cold-responsive genes were identified, of which, 6 are involved in regulating biological processes in chloroplasts, including the reported EF-Tu, Prk, and ChlD, and 8 are involved in the protein synthesis and degradation processes. Differential expression of these genes between NIL(qcss12) and its controls under cold stress may be responsible for qCSS12-mediated cold tolerance in japonica rice. Moreover, natural variations in 12 of these hub genes are highly correlated with the cold tolerance divergence in two rice subspecies. The results provide deep insights into a better understanding of the molecular basis of cold adaptation in rice and provide a theoretical basis for molecular breeding.

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Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2022), and China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA011931) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa. The other datasets generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

The authors thank Prof. Hongxuan Lin (Institute of Plant physiology and Ecology, Shanghai, China) and Prof. Wensheng Wang (Chinese Academy of Agricultural Sciences, Beijing, China) for kindly providing the rice materials for this study.

Funding

This work was supported by the National Natural Science Foundation of China (CN) (31671646), the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (SKLCUSA-a08), the Talent, Science, and technology projects (Barenke-20220001), and the Natural Science Foundation of Guangxi Province (2018GXNSFDA138004).

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Authors and Affiliations

  1. College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China

    Ping Gan, Xianglan Luo, Hanxing Wei, Yunfei Hu & Jijing Luo

  2. College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China

    Rongbai Li

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  1. Ping Gan
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  2. Xianglan Luo
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  3. Hanxing Wei
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  4. Yunfei Hu
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  6. Jijing Luo
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Contributions

JL, PG, and RL conceived and designed the experiments. PG and HW performed all the lab experiments. PG, XL, and HW conducted the field trials and collected the samples for RNA-Seq. PG and YH performed WGCNA and data processing. PG drafted the manuscript. JL revised the manuscript. All the authors read and approved the final version of the manuscript.

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Correspondence to Jijing Luo.

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Communicated by Haitao Shi.

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Gan, P., Luo, X., Wei, H. et al. Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA. Plant Cell Rep 43, 24 (2024). https://doi.org/10.1007/s00299-023-03093-8

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