Genome-wide identification and expression analysis of phytochrome gene family in Aikang58 wheat ( L.).
Journal:
Frontiers in plant science
Published Date:
Jan 21, 2025
Abstract
Phytochromes are essential photoreceptors in plants that sense red and far-red light, playing a vital role in regulating plant growth and development through light signal transduction. Despite extensive research on phytochromes in model plants like and rice, they have received relatively little attention in wheat. In this study, we employed bioinformatics methods to identify eight genes in the Aikang58 wheat variety. Based on gene structure, conserved domains, and phylogenetic relationships, the gene family exhibits a high degree of conservation. Synteny analysis revealed the evolutionary history of the genes in Aikang58 and Chinese Spring wheat ( L.), barley ( L.), rice ( L.), maize ( L.), quinoa ( Willd.), soybean [ (L.) Merr.], and [ (L.) Heynh.]. Among these species, wheat is most closely related to barley, followed by rice and maize. The -acting element analysis indicates that the promoter regions of genes contain a large number of CAT-box, CGTCA-motif, GC-motif, etc., which are mainly involved in plant development, hormone response, and stress response. Gene expression profiling demonstrated that genes exhibit varying expression levels across different tissues and are induced by various stress conditions and plant hormone treatments. Co-expression network analysis suggested that genes may specifically regulate downstream genes associated with stress responses, chloroplast development, and circadian rhythms. Additionally, the least absolute shrinkage and selection operator (LASSO) regression algorithm in machine learning was used to screen transcription factors such as bHLH, WRKY, and MYB that influenced the expression of genes. This method helps to quickly extract key influencing factors from a large amount of complex data. Overall, these findings provide new insights into the role of phytochromes in wheat growth, development, and stress responses, laying a foundation for future research on phytochromes in wheat.
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