Genome-wide identification and drought-responsive root expression profiling of the VQ gene family in proso millet ( Panicum miliaceum L.)

Background Proso millet ( Panicum miliaceum L.) is a drought-tolerant cereal crop cultivated in arid and semi-arid regions. VQ proteins, a class of plant-specific proteins characterized by a conserved VQ motif (FxxxVQxxTG), are known to play critical roles in plant responses to abiotic stress. To elucidate the genetic basis of drought tolerance in proso millet, a genome-wide identification and characterization of the VQ gene family was undertaken. Methods This study involved the identification of all VQ family members from the proso millet genome, followed by comprehensive analyses including chromosomal localization, phylogenetic relationships, gene structure, conserved motifs, collinearity, and promoter cis -acting elements. Expression profiling was conducted using transcriptomics and Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) to investigate potential gene functions. Additionally, the drought tolerance of various germplasm materials was systematically assessed. Results A total of 70 VQ genes ( PmVQ1 – PmVQ70 ) were identified and classified into four distinct subfamilies. Based on the screening of root-preferential and drought-responsive candidate genes, combined with phenotypic and qRT-PCR analyses of drought-tolerant and drought-sensitive materials, four key candidate genes were identified. qRT-PCR analysis revealed that the four genes exhibited differential expression patterns between drought-tolerant and drought-sensitive materials, suggesting their potential roles as core regulators in proso millet’s drought response, particularly in root-specific regulatory pathways under drought stress. This study provides a systematic analysis of the VQ gene family in proso millet and offers valuable genetic resources for elucidating drought tolerance mechanisms and advancing molecular breeding.