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Pathogenesis-related protein-4 (PR-4) gene family in Qingke (Hordeum vulgare L. var. nudum): genome-wide identification, structural analysis and expression profile under stresses

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Abstract

Background

Pathogenesis-related (PR) proteins are active participants of plant defense against biotic and abiotic stresses. The PR-4 family features a Barwin domain at the C-terminus, which endows the host plant with disease resistance. However, comprehensive analysis of PR-4 genes is still lacking in Qingke (Hordeum vulgare L. var. nudum).

Methods and results

Herein, a total of four PR-4 genes were identified from the genome of Qingke through HMM profiling. Devoid of the chitin-binding domain, these 4 proteins were grouped as class II PR-4s. Phylogenic analysis revealed that 127 PR-4s from 47 species were clustered into 3 major groups, among which the four Qingke PR-4s were claded into group I. Analysis of gene structure demonstrated that no intron was found in 3 out of the 4 Qingke PR-4s, and HOVUSG0928500 was the only gene contained one intron. An array of cis-acting motifs were detected in promoters of Qingke PR-4 genes, including elements associated with hormone response, light response, stress response, growth and development processes and binding sites of transcription factors, implying their diverse role. Expression profiling confirmed that Qingke PR-4s were involved in defense response against drought, cold and powdery mildews infection, and transcription of HOVUSG1974300 and HOVUSG5705400 was differentially regulated by MeJA and SA.

Conclusion

Findings of the study provided insights into the genetic basis of the PR-4 family genes, and would promote further investigation on protein function and utilization.

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Funding

This research was supported by Science and Technology Project of Qinghai Province (2019-ZJ-962Q). Dr. Le Wang was supported by the ‘Kunlun Elite-Innovation & Carving out Talent’ program of Qinghai Province.

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Authors and Affiliations

  1. State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, 810016, China

    Le Wang, Qianhan Shang, Wei Yin, Wei Sa & Jian Liang

  2. College of Eco-Environmental Engineering, Qinghai University, Xi’ning, 810016, China

    Le Wang, Hailing Lu, Jiarong Zhan, Qianhan Shang & Jian Liang

  3. Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, 810016, Xi’ning, China

    Le Wang, Qianhan Shang, Li Wang & Jian Liang

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  1. Le Wang
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  2. Hailing Lu
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Contributions

Conceived and designed the experiments: LW, JL. Performed bioinformatic analysis: LW, HL, JZ, QS. Wrote the paper: LW, JL, LW, WY, WS.

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Correspondence to Jian Liang.

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Wang, L., Lu, H., Zhan, J. et al. Pathogenesis-related protein-4 (PR-4) gene family in Qingke (Hordeum vulgare L. var. nudum): genome-wide identification, structural analysis and expression profile under stresses. Mol Biol Rep 49, 9397–9408 (2022). https://doi.org/10.1007/s11033-022-07794-3

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