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Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time

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Abstract

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111 PHD genes were newly identified in rye genome and ScPHD5’s role in regulating cold tolerance and flowering time was suggested.

Abstract

Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

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Funding

This work was supported by the Basic Science Research Program through the National Research Foundation of Korea, funded by the Ministry of Education (2021R1I1A1A01048945) and by a grant from Korea University.

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Authors and Affiliations

  1. Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Korea

    Woo Joo Jung

  2. Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea

    Ji Hyeon Jeong & Yong Weon Seo

  3. Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea

    Jin Seok Yoon & Yong Weon Seo

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WJJ and YWS conceived and planned the experiments. WJJ, JHJ, and JSY performed the experiments. WJJ wrote the draft manuscript. All authors provided critical feedback and helped shape the research, analysis, and manuscript.

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Jung, W.J., Jeong, J.H., Yoon, J.S. et al. Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time. Plant Cell Rep 43, 142 (2024). https://doi.org/10.1007/s00299-024-03226-7

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