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Genome-wide identification of PEBP gene family members in potato, their phylogenetic relationships, and expression patterns under heat stress

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Abstract

Background

The phosphatidylethanolamine-binding protein (PEBP) gene family is involved in regulating many plant traits. Genome-wide identification of PEPB members and knowledge of their responses to heat stress may assist genetic improvement of potato (Solanum tuberosum).

Methods and results

We identified PEBP gene family members from both the recently-updated, long-reads-based reference genome (DM v6.1) and the previous short-reads-based annotation (PGSC DM v3.4) of the potato reference genome and characterized their heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP family genes were identified from DM v6.1 and named as StPEBP1 to StPEBP15 based on their locations on 6 chromosomes and were classified into FT, TFL, MFT, and PEBP-like subfamilies. Most of the StPEBP genes were found to have conserved motifs 1 to 5. Tandem or segmental duplications were found between StPEBP genes in seven pairs. Heat stress induced opposite expression patterns of certain FT and TFL members but involving different members in leaves, roots and tubers.

Conclusion

The long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP family genes. Heat stress tends to decrease FT gene activities but increases TFL gene activities, but this opposite expression involves different FT/TFL pairs in leaves, roots, and tubers. This tissue-specific expression pattern of PEBP members may partly explain why different potato organs differ in their sensitivities to heat stress. Our study provides candidate PEBP family genes and relevant information for genetic improvement of heat tolerance in potato and may help understand heat-induced responses in other plants.

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Acknowledgements

This research was supported by National Natural Science Foundation of China (No. 31860399) to Huaijun Si, Natural Sciences and Engineering Research Council of Canada Discovery Grant (RGPIN 2017-04589) to Om P. Rajora, and the Agriculture and Agri-Food Canada (AAFC) support to Xiu-Qing Li at the Fredericton Research and Development Centre, AAFC, Government of Canada. We thank the China Scholarship Council of the P. R. China for the financial support to Guodong Zhang, a PhD student under the Joint PhD training program between AAFC and Education Ministry of P.R. China.

Funding

Funding was provided by National Natural Science Foundation of China (31860399), Agriculture and Agri-Food Canada (A-base research funding) and Natural Sciences and Engineering Research Council of Canada (RGPIN 2017-04589).

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Authors and Affiliations

  1. College of Agronomy, Gansu Agricultural University, Lanzhou, China

    Guodong Zhang

  2. Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi, China

    Guodong Zhang

  3. Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China

    Guodong Zhang, Xin Jin, Ning Zhang & Huaijun Si

  4. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada

    Guodong Zhang & Xiu-Qing Li

  5. College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China

    Xin Jin, Ning Zhang & Huaijun Si

  6. Rizhao Academy of Agricultural Sciences, Rizhao, China

    Xiubao Li

  7. Qingdao Customs of the People’s Republication of China, Shinan, Qingdao, 266001, China

    Shaoqian Li

  8. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada

    Om P. Rajora

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  1. Guodong Zhang
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  2. Xin Jin
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  3. Xiubao Li
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Contributions

GZ and HS designed the study and drafted the manuscript, GZ and XJ conducted the analysis and experiments, XL, NZ, SL, HS, OPR and XQL contributed to discussion and data interpretation, OPR and XQL revised and reshaped the manuscript and contributed to the overall direction of the manuscript. All authors approved the manuscript.

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Correspondence to Huaijun Si, Om P. Rajora or Xiu-Qing Li.

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Zhang, G., Jin, X., Li, X. et al. Genome-wide identification of PEBP gene family members in potato, their phylogenetic relationships, and expression patterns under heat stress. Mol Biol Rep 49, 4683–4697 (2022). https://doi.org/10.1007/s11033-022-07318-z

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