Genome-Wide Identification and Expression Profile of the HD-Zip Transcription Factor Family Associated with Seed Germination and Abiotic Stress Response in Miscanthus sinensis

Jiayi Chen; Qifan Ran; Zhongfu Yang; Ying Zhou; Zhihang Yuan; Huiqi Lai; Jing Wang; Gang Nie; Yongqun Zhu

doi:10.3390/genes13122256

Genome-Wide Identification and Expression Profile of the HD-Zip Transcription Factor Family Associated with Seed Germination and Abiotic Stress Response in Miscanthus sinensis

Genes (Basel). 2022 Nov 30;13(12):2256. doi: 10.3390/genes13122256.

Authors

Jiayi Chen¹, Qifan Ran², Zhongfu Yang¹, Ying Zhou¹, Zhihang Yuan¹, Huiqi Lai¹, Jing Wang¹, Gang Nie¹, Yongqun Zhu³

Affiliations

¹ Department of Forage Breeding and Cultivation, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
² Institute of Grassland Sciences, Chongqing Academy of Animal Science, Chongqing 402460, China.
³ Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.

Abstract

Miscanthus sinensis is an ornamental grass, non-food bioenergy crop, and forage with high feeding value. It can adapt to many kinds of soil conditions due to its high level of resistance to various abiotic stresses. However, a low level of seed germination restricts the utilization and application of M. sinensis. It is reported that the Homeodomain-leucine zipper (HD-Zip) gene family participates in plant growth and development and ability to cope with outside environment stresses, which may potentially regulate seed germination and stress resistance in M. sinensis. In this study, a complete overview of M. sinensis HD-Zip genes was conducted, including gene structure, conserved motifs, chromosomal distribution, and gene duplication patterns. A total of 169 members were identified, and the HD-Zip proteins were divided into four subgroups. Inter-chromosomal evolutionary analysis revealed that four pairs of tandem duplicate genes and 72 segmental duplications were detected, suggesting the possible role of gene replication events in the amplification of the M. sinensis HD-Zip gene family. There was an uneven distribution of HD-Zip genes on 19 chromosomes of M. sinensis. Also, evolutionary analysis showed that M. sinensis HD-Zip gene family members had more collinearity with monocotyledons and less with dicotyledons. The gene structure analysis showed that there were 93.5% of proteins with motif 1 and motif 4, while motif 10 was only found in group IV. Based on the cis-elements analysis, it appeared that most of the genes were related to plant growth and development, various hormones, and abiotic stress. Furthermore, qRT-PCR analysis showed that Misin06G303300.1 was significantly expressed in seed germination and Misin05G030000.1 and Misin06G303300.1 were highly expressed under chromium, salt, and drought stress. Results in this study will provide a basis for further exploring the potential role of HD-Zip genes in stress responses and genetic improvement of M. sinensis seed germination.

Keywords: HD-Zip transcription factor; Miscanthus sinensis; abiotic stress; gene expression; seed germination.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Germination* / genetics
Poaceae / genetics
Poaceae / metabolism
Seeds / metabolism
Stress, Physiological / genetics
Transcription Factors* / metabolism

Substances

Transcription Factors

Grants and funding

This work was supported by the earmarked fund for CARS (CARS-34), Agricultural Science and Technology Achievement Transformation Project in Sichuan Province (2021NZZJ0004) and Sichuan Forage Grass Innovation Team (SCCXTD-2020-16).