Pan-genome-wide identification and evolutionary analysis of SPX gene family reveal distinct phosphorus adaptation regulatory strategies in foxtail millet

Abstract Background Phosphorus (P) is an essential macronutrient, and SPX domain-containing proteins are central regulators of phosphate homeostasis in plants. Foxtail millet (Setaria italica) is renowned for its exceptional nutrient-use efficiency under low-fertility soils; however, its SPX gene family remains largely uncharacterized at the genome level. A pan-genome-wide investigation is therefore required to reveal the evolutionary and regulatory basis of phosphorus adaptation in this agronomically important cereal. Results In this study, we conducted a comprehensive pan-genomic analysis of 114 diverse germplasm accessions of foxtail millet, and identified 1646 SiSPX genes. These genes were phylogenetically classified into four distinct subfamilies, SPX, SPX-EXS, SPX-MFS, and SPX-RING. Evolutionary analyses revealed pervasive purifying selection (Ka/Ks < 1) across the entire family, while lineage-specific expansions within the SPX-MFS and SPX-RING subfamilies suggested adaptive diversification during domestication. Cis-regulatory element profiling uncovered subfamily-specific enrichment of P1BS motifs, with SPX subfamily members harboring up to five Pi-starvation-responsive elements. Under low-P stress, root-specific SiSPX-MFS genes, notably SiSPX-MFS2, exhibited progressive upregulation, correlating with stress duration, while core SPX subfamily members (SiSPX2/3/6/13) showed significant root-specific induction. Weighted gene co-expression network analysis (WGCNA) further implicated these genes in transcriptional modules involving key transcription factors such as NAC, WRKY, and bHLH, highlighting their synergistic roles in P signaling. Interestingly, the SPX-RING subfamily displayed a notable absence of P1BS elements but a significant enrichment of MYB-binding motifs, suggesting alternative regulatory strategies for P adaptation. Conclusions This study provides the first pan-genomic resource for foxtail millet SPX genes, deciphers their functional divergence in P adaptation, and identifies promising targets for enhancing crop resilience and phosphorus-use efficiency in nutrient-limited agricultural systems.