Apple fruit acidity which considerably affects fruit taste and flavor is primarily determined by malate concentrations. Previous studies reported that apple fruit acidity was predominantly controlled by the major QTL Ma. To better understand apple fruit acidity, this study attempts to identify and characterize the gene underpinning Ma and its associated co-expression gene networks. To achieve the goal, three sets of experiments were conducted. The first set of experiments was designed to identify the candidate gene for Ma and was summarized in Chapter 1. This chapter presents that the Ma locus physically spans over 65kb and harbors two aluminum-activated malate transporter (ALMT) -like genes, designated Ma1 and Ma2. Other important findings include 1) only Ma1 was expressed in significant correlation with the variation of acid levels, and 2) there is a nucleotide mutation that leads to a pre-mature stop codon in Ma1.Overall, it concludes that Ma1 rather than Ma2 is the gene underlying Ma. The second set of experiments aims at identification of the Ma1 associated coexpression gene network regulating malate levels in developing fruit of Golden Delicious and was reported in Chapter 3. One finding of this chapter is that malatepyruvate interconversion, photosynthesis, mitochondrial electron transport, and amino acid degradation were important pathways for the change of malate levels in developing fruit. The other finding is that symplastic signal transduction, transcriptional regulation, post-translational modification and apoplastic roles were important in the regulation of fruit acidity. The third set of experiments was conducted to identify the Ma1 associated coexpression gene network controlling acidity in mature fruit of ten diverse apples and was described in Chapter 4. Data in this chapter suggested that calcium signaling was likely a crucial mechanism that regulates both the expression of Ma1 and the Ma1 associated co-expression gene network governing fruit acidity. Chapter 2 is about improving the current version of apple reference transcriptome due to its unaccep low coverage in mapping of RNA-seq reads. The improved apple reference transcriptome comprises 71,178 genes (17,524 are novel) and increases the coverage of RNA-seq reads from 37-46% to 62-82%. This chapter lays a foundation for data analysis in Chapters 3 and 4. In conclusion, this study takes the understanding of apple fruit acidity to a higher level and opens more grounds for further dedicated studies.