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Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality. However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are 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 functions and biochemical properties were analyzed. A chromosomal 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 undergone strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies. In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes 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. Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit. The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

Auxin (indole-3-acetic acid, IAA) has a considerable impact on the regulation of plant carbohydrate levels and growth, but the mechanism by which it regulates sugar levels in plants has received little attention. In this study, we found that exogenous IAA altered fructose (Fru), glucose (Glc), and sucrose (Suc) concentrations in shoot tips mainly by regulating MdSUSY1, MdFRK2, MdHxK1 and MdSDH2 transcript levels. Additionally, we used 5-year-old ‘Royal Gala’ apple trees to further verify that these genes play primary roles in regulating sink strength. The results showed that MdSUSY1, MdFRK2, MdHxK1/3 and MdSDH2 might be major contributors to sink strength regulation. Taken together, these results provide new insight into the regulation of the carbohydrate metabolism mechanism, which will be helpful for regulating sink strength and yield.

Hexokinase (HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes. However, the evolutionary pattern of the HXK gene family in apple remains unknown. In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1. The physiological and biochemical properties, exonintron structures, conserved motifs, and cis-elements of the MdHXK genes were determined. Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus. Gene duplication revealed that whole-genome duplication (WGD) and segmental duplication played vital roles in MdHXK gene family expansion. The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication. Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis. Different evolutionary rates were estimated among the various HXK subfamilies. Moreover, divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation. Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.

Sucrose synthases (SUS) are a family of enzymes that play pivotal roles in carbon partitioning, sink strength and plant development. A total of 11 SUS genes have been identified in the genome of Malus domestica (MdSUSs), and phylogenetic analysis revealed that the MdSUS genes were divided into three groups, named as SUS I, SUS II and SUS III, respectively. The SUS I and SUS III groups included four homologs each, whereas the SUS II group contained three homologs. SUS genes in the same group showed similar structural characteristics, such as exon number, size and length distribution. After assessing four different tissues, MdSUS1s and MdSUS2.1 showed the highest expression in fruit, whereas MdSUS2.2/2.3 and MdSUS3s exhibit the highest expression in shoot tips. Most MdSUSs showed decreased expression during fruit development, similar to SUS enzyme activity, but both MdSUS2.1 and MdSUS1.4 displayed opposite expression profiles. These results suggest that different MdSUS genes might play distinct roles in the sink-source sugar cycle and sugar utilization in apple sink tissues.

indica and japonica are the two most important subspecies of Asian cultivated rice. Identifying mechanisms responsible for population differentiation in these subspecies is important for indica-japonica hybridization breeding. In this study, subspecies and economic trait differentiation patterns were analyzed using morphological and molecular (InDel and Intron Length Polymorphism) data in F2 and F3 populations derived from indica-japonica hybridization. Populations were grown in Liaoning and Guangdong provinces, China, with F3 populations generated from F2 populations using bulk harvesting (BM) and single-seed descent methods (SSD). Segregation distortion was detected in F3-BM populations, but not in F3-SSD or in F2 populations. Superior performance was observed with respect to economic traits in Liaoning compared with that in Guangdong and 1 000-grain weight (KW), seed setting rate (SSR) and grain yield per plant (GYP) were significantly correlated with indica and japonica subspecies types. Analysis of molecular and morphological data demonstrated that the environment is the main factor giving rise to population differentiation in indica-japonica hybridization. In addition, we also found that KW, SSR and GYP are related to subspecies characteristics and kinship, which is possibly a significant factor resulting in economic trait differentiation and determining environmental adaptability. Our study has provided new insights into the process of population differentiation in these subspecies to inform indica-japonica hybridization breeding.