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Comparative Transcriptome Profile Analysis of Anther Development in Reproductive Stage of Rice in Cold Region Under Cold Stress

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Abstract

Rice in cold region is threatened by cold stress frequently, resulting in severe losses of rice production. In the present study, two rice varieties with contrast cold tolerance in the reproductive stage (Longjing25, cold tolerant; Longjing11 cold sensitive) were compared using RNA-seq technique. A total of 14,861 and 12,148 differentially expressed genes (DEGs) were obtained by comparison of LJ25 and LJ11 after 2 days and 4 days of cold stress challenge. Subsequent Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that five significant pathways were specifically enriched in LJ11. Starch and sucrose metabolism was the only one significant pathway (containing 47 DEGs) annotated in both of varieties during two cold treatment periods. By weighted gene co-expression network analysis (WGCNA), 14 co-expression gene modules were calculated, among which turquoise, cyan, and dark green were the most concerned modules, containing 4807, 2682, and 1174 DEGs, respectively. Finally, we analyzed the transcriptional factors (TFs), and TF families of MYB, zinc finger, AP2/ERF-AP2, bHLH, NAC, bZIP, and WRKY were the biggest seven subfamilies. Collectively, our findings provided valuable insights into the molecular and genetic mechanisms responsible for rice’s response to cold stress.

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Funding

This study was supported by the National Key Research and Development Plan (2016YFD0101801), the Modern Agro-industry Technology Research System (CARS-01-09), and the Science and Technology Support of the Ministry of Science and Technology (2015BAD02B01-3).

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  1. Zhenhua Guo and Chuanxue Liu contributed equally to this work.

Authors and Affiliations

  1. National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China

    Zhenhua Guo, Wuming Xiao & Zhiqiang Chen

  2. Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, China

    Zhenhua Guo, Chuanxue Liu, Ruiying Wang, Lanming Zhang, Shiwu Guan, Shuhua Zhang, Xiaoqun Huang, Junxiang Guo, Xuesong Zhou, Xiaodong Du & Guojun Pan

  3. Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China

    Lijun Cai

  4. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China

    Hao Liu

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  1. Zhenhua Guo
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  2. Chuanxue Liu
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  11. Junxiang Guo
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  14. Guojun Pan
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  15. Zhiqiang Chen
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Contributions

ZG and CL conceived the original screening and research plans. GP and ZC supervised the experiments. ZG, RW, WX, LZ, SG, XH, XZ, JG, and XD performed most of the experiments. ZG, SZ, and LC designed the experiments and analyzed the data. ZG conceived the project and wrote the article. ZG and HL supervised and complemented the writing. All authors read and approved the final version of the paper.

Corresponding authors

Correspondence to Guojun Pan or Zhiqiang Chen.

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The authors declare that they have no conflict of interest.

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Table S1

Gene expression in LJ11 and LJ25. (XLSX 2389 kb)

Table S2

All-time courses of gene expression in Longing25. (XLSX 1266 kb)

Table S3

All-time courses of gene expression in LJ11. (XLSX 1332 kb)

Table S4

DEGs in Longjng25 after 2 days and 4 days of cold stress challenge. (XLSX 653 kb)

Table S5

GO analysis of DEGs in LJ25 after 2 days and 4 days of cold stress challenge. (XLS 43 kb)

Table S6

DEGs in KEGG pathway of plant hormone signal transduction in LJ25 under cold stress. (XLSX 15 kb)

Table S7

DEGs in Longjng11 after 2 days and 4 days of cold stress challenge. (XLSX 1343 kb)

Table S8

GO analysis of DEGs in LJ11 in the entire cold stress treatment. (XLSX 24 kb)

Table S9

DEGs in KEGG pathway of carbon fixation in photosynthetic organisms in LJ11 under cold stress. (XLSX 13 kb)

Table S10

DEGs between LJ25 and LJ11 after 2 days of cold stress challenge. (XLSX 1390 kb)

Table S11

DEGs between LJ25 and LJ11 after 4 days of cold stress challenge. (XLSX 1117 kb)

Table S12

Common DEGs in KEGG pathway of starch and sucrose metabolism in LJ25 and LJ11. (XLSX 17 kb)

Table S13

DEGs in turquoise module of WGCNA. (XLSX 89 kb)

Table S14

DEGs in cyan module of WGCNA. (XLSX 54 kb)

Table S15

DEGs in darkgreen module of WGCNA. (XLSX 29 kb)

Table S16

Enrichment pathway in turquoise, cyan and darkgreen modules of WGCNA. (XLSX 12 kb)

Table S17

TFs in LJ25 and lJ11 after cold stress treatment (XLSX 160 kb)

Table S18

7 top TFs in LJ25 and LJ11 after cold stress treatment (XLSX 108 kb)

Table S19

Primers of eight DEGs for qRT-PCR validation (XLSX 9 kb)

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Guo, Z., Liu, C., Xiao, W. et al. Comparative Transcriptome Profile Analysis of Anther Development in Reproductive Stage of Rice in Cold Region Under Cold Stress. Plant Mol Biol Rep 37, 129–145 (2019). https://doi.org/10.1007/s11105-019-01137-6

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