Genome‑Wide Identification and Expression Analysis of SPX Domain-Containing Gene Subfamily in Response to Phosphorus-Solubilizing Bacteria in Apple (Malus domestica)

Phosphate is one of the major elements that significantly affects fruit yield and quality. The aim of the study was to determine whether using phosphorus-solubilizing bacteria could produce high-quality apple nursery trees. Five different treatments were tested on a “Granny Smith” apple cultivar that was grafted onto an M.9 rootstock. These were 100% P, 50% P, 50% P + Bacillus megatarum (plant growth promoting rhizobacteria, PGPR), 0%P, and 0%P + PGPR. The study also identified the SPX gene family, which is essential for plant growth and development and responds to phosphorus (P) stress. A total of 72 SPX genes were identified in different plant species based on structural and phylogenetic analysis. The apple genome contains seven different SPX genes distributed on five of the 17 chromosomes. Gene structure and motif analysis showed that SPX genes show a relatively conserved exon/intron arrangement and motif composition in five different species: apple, strawberry, peach, apricot, and grape. Protein–protein network analysis showed that SPX proteins are closely related to proteins involved in P metabolism in apple. The digital expression profiles of MdSPX genes among 47 apple tissues were characterized to provide insight into their potential functions. RT-qPCR revealed that the expression level of all MdSPXs was significantly downregulated in 50% P + PGPR treatments, indicating that 50% P combined with PGPR is effectively taken up by the plant, saving it from Pi starvation. These results not only confirm the key role of MdSPXs in Pi homeostasis and the Pi signaling pathway but also clarify the importance of Pi-solubilizing bacteria in plant nutrition.