Genome-wide identification of Zinc Finger-Homeodomain (ZF-HD) gene family and expression analysis during abiotic stress in rye

Adverse environmental conditions, encompassing both biotic and abiotic stresses, are critical factors that significantly impact the normal growth and development of plants worldwide, leading to increasingly severe consequences in recent years. To counteract the detrimental effects of these stresses, plants possess a multitude of resistance genes. The zinc finger homeodomain (ZF-HD) protein family plays a pivotal role as transcription factors, participating in responses to biotic and abiotic stresses, regulating plant growth and development, and mediating hormonal signaling pathways. Rye (Secale cereale), known for its robust tolerance to various abiotic stresses such as low temperature, drought, poor soil fertility, and salinity, has yet to be thoroughly investigated regarding the functional roles of ZF-HD genes in stress resistance regulation. In this study, a total of 22 ScZF-HD genes were identified within the rye genome. Phylogenetic analysis revealed that these genes could be categorized into six distinct groups (Groups I-VI). Based on conserved domain characteristics, the ScZF-HD genes were further classified into two subfamilies: ScZHD and ScMIF. Transcriptomic analysis of various rye tissues demonstrated that ZF-HD genes exhibit high expression levels primarily during spikelet formation, anthesis, and grain filling stages, suggesting their significant regulatory roles in floral and grain development. To further elucidate the expression patterns of ScZF-HDs under stress conditions, qRT-PCR assays were conducted under drought, low temperature, and salt stress treatments. The results revealed that ScZHD1, ScZHD3, ScZHD5, ScZHD6, ScZHD7, ScZHD9, ScZHD12, ScMIF5, ScMIF6, and ScMIF7 were up-regulated under drought stress. Similarly, ScZHD1, ScZHD5, ScZHD6, ScZHD7, ScZHD8, ScZHD9, ScZHD10, ScZHD12, ScMIF5, ScMIF6, and ScMIF7 showed increased expression under low temperature stress. Under salt stress, ScZHD1, ScZHD5, ScZHD6, ScZHD7, ScZHD9, ScZHD12, and ScMIF5 were up-regulated. These findings provide valuable insights into the potential biological functions of ScZF-HD genes in rye and lay the groundwork for further functional characterization and stress resistance breeding in cereal crop.