Transcriptomic analysis reveals key genes regulating organic acid synthesis and accumulation in the pulp of Litchi chinensis Sonn. cv. Feizixiao

• Determining the kinds of the organic acids in the pulp of Feizixiao litchi and observing the dynamic change characteristics of the different organic acids content. • Identifing the key biochemical pathways for the metabolism of the organic acids in the pulp of Feizixiao litchi through RNA-seq. • Confirming the key genes regulating the organic acids accumulation in the pulp of Feizixiao litchi and their expressions characteristics through RNA-seq. • Verifing the expression of the above key genes through real-time fluorescence quantitative PCR. To investigate the gene expression characteristics and patterns of organic acid synthesis and accumulation in the pulp of Litchi chinensis Sonn. cv. Feizixiao (FZX), 16-year-old Feizixiao litchi trees were used as the experimental material, and the dynamic changes in the main organic acids in the pulp were determined for two years. RNA sequencing was carried out when the total acids in the pulp changed drastically 35, 50 and 73 d after anthesis in 2020 to discover the molecular mechanism of the synthesis and accumulation of different organic acids in pulp. The results indicate that tartaric acid and malic acid were the main organic acids in pulp. The RNA-seq contained 165,886 transcripts, and 12 176, 19 835 and 5 048 DEGs were observed in the 35 d vs. 50 d, 35 d vs. 73 d and 50 d vs. 73 d groups, respectively. These expressed transcripts of organic acid metabolism were significantly enriched in correlated pathways, including glycolysis and gluconeogenesis, citric acid cycle (TCA cycle), and ascorbate and aldarate metabolism. In this paper, 75 genes of the enzymes related to organic acid metabolic pathways were screened, and these enzymes included PEPC, MDH, ME, CS, IDH and ACO. Ten unigenes were selected to confirm by real-time PCR, and the linear regression between the RNA-Seq results and real-time PCR data was significant ( r = 0.8637). In addition, the expression of PEPC and ACO genes was consistent with the content of citric acid, the expression of the CS gene increased with time, and the change in expression of the MDH gene was similar to that of the malic acid content, while the expression of the ME gene showed an opposite trend. Therefore, it was possible to regulate acid accumulation in pulp by regulating the expression of key genes related to pathways such as the TCA cycle, and then the comprehensive fruit quality was regulated.