Genome-wide identification and expression analysis of the SPX gene family in rice under phosphorus treatment

This study aimed to systematically identify the rice SPX gene family at the whole-genome level, characterize its evolutionary features and expression patterns, and provide a basis for elucidating SPX functions in phosphorus signal transduction. Bioinformatics approaches were used to identify SPX genes in rice and to analyze their physicochemical properties, phylogenetic relationships, gene structures, conserved motifs, promoter cis-acting elements, and collinearity. Transcriptomic data and quantitative real-time PCR (RT-qPCR) were used to examine tissue-specific expression and responses to phosphorus stress. Six SPX genes were identified and mapped to five chromosomes. Phylogenetic analysis showed that OsSPX1 and OsSPX2 clustered together with 100% bootstrap support, whereas OsSPX3 formed a well-supported subclade with OsSPX5 and OsSPX6. Collinearity analysis identified two segmental duplication pairs (OsSPX1/OsSPX2 and OsSPX5/OsSPX6), and all Ka/Ks values were < 1 (0.19-0.44), indicating strong purifying selection. Gene structure analysis showed that OsSPX members contain 2-3 exons, and conserved motif distributions were highly consistent with the phylogenetic relationships. Promoter analysis identified 135 cis-acting elements, mainly related to hormone, light, and stress responses, with methyl jasmonate- and abscisic acid-responsive elements being the most abundant. RT-qPCR analysis in the ShijinB variety indicated that OsSPX1-OsSPX6 were preferentially expressed in roots, with OsSPX3 also showing relatively high expression in inflorescences and OsSPX1 and OsSPX4 showing relatively high expression in leaves. Under low-phosphorus conditions, OsSPX1, OsSPX2, OsSPX3, OsSPX5, and OsSPX6 were significantly upregulated, with OsSPX3 showing the strongest induction, whereas OsSPX4 was not affected by phosphorus availability. Overall, the rice SPX gene family appears to have expanded via segmental duplication and subsequently evolved under purifying selection; although gene structures and motif compositions are relatively conserved, members show clear tissue specificity and differential responsiveness to phosphorus stress.