Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

Sucrose phosphate synthase (SPS), as a rate-limiting enzyme working in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, plays an essential role in energy provision during growth and development as well as improving fruit quality in plants. However, the systematic analysis and evolutionary pattern of the SPS gene family in apple still lacking. In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1. The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological and biochemical properties were analyzed. Chromosome location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion. The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have suffered from strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified on the basis of phylogenetic relationship, old gene duplication and significantly divergent evolutionary rates among the SPS gene subfamilies were observed. In addition, a major gene MdSPSA2.3 related to sucrose accumulation were identified according to the highly consistent change trends of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development. Further, the virus-induced silencing of MdSPSA2.3 confirmed the function of MdSPSA2.3 in sucrose accumulation of apple fruit. The present study lays a theoretical foundation to better clarify the biological functions of the MdSPS genes during apple fruit development.