Genome-wide identification of the PIF gene family in broomcorn millet (Panicum miliaceum) highlights PmPIF5 as a candidate regulator of photoperiod responses.

Abstract

Background: Phytochrome-interacting factors (PIFs) are central bHLH transcription factors that link light perception to developmental programs and stress response. Although PIFs have been characterized in several model and crop species, their family composition and potential roles in broomcorn millet remain unknown.

Results: Based on the AJ08 reference genome, publicly available transcriptome datasets, and resequencing variants from 516 accessions, we conducted an integrated analysis combining genome-wide identification, comparative genomics, expression profiling, RT-qPCR validation, and haplotype analysis. We identified 15 PmPIF genes that were unevenly distributed across 11 chromosomes and could be classified into four phylogenetic groups (Groups 1-4). All PmPIF proteins harbored a conserved bHLH domain and were predicted to localize in the nucleus; secondary structure prediction indicated that α-helices and random coils were predominant. Promoter analyses revealed abundant cis-acting elements related to light responsiveness, phytohormone signaling, and stress responses. Expression analyses under contrasting photoperiod treatments showed pronounced divergence among PmPIF members, with PmPIF5 consistently showing differential expression across multiple comparisons. KEGG enrichment implicated PmPIF5 in the circadian rhythm-plant pathway, and correlation analyses revealed significant associations between PmPIF5 and several light signaling-related genes, including PRR73, UVR8, GHD7, and COL13. Population-level haplotype analysis of PmPIF5 detected five haplotypes among the 516 accessions, with Hap1 being the predominant haplotype (74.42%).

Conclusions: This study provides a comprehensive resource for the PmPIF gene family in broomcorn millet and suggests that PmPIF5 is a promising candidate gene involved in photoperiod-related regulation. These findings lay the foundation for functional validation and support molecular breeding for photoperiod adaptation in broomcorn millet.