Transcriptome and Metabolome Analyses Reveal Sugar and Acid Accumulation during Apricot Fruit Development

Abstract

The apricot (Prunus armeniaca L.) is a fruit that belongs to the Rosaceae family; it has a unique flavor and is of important economic and nutritional value. The composition and content of soluble sugars and organic acids in fruit are key factors in determining the flavor quality. However, the molecular mechanism of sugar and acid accumulation in apricots remains unclear. We measured sucrose, fructose, glucose, sorbitol, starch, malate, citric acid, titratable acid, and pH, and investigated the transcriptome profiles of three apricots (the high-sugar cultivar 'Shushanggan', common-sugar cultivar 'Sungold', and low-sugar cultivar 'F43') at three distinct developmental phases. The findings indicated that 'Shushanggan' accumulates a greater amount of sucrose, glucose, fructose, and sorbitol, and less citric acid and titratable acid, resulting in a better flavor; 'Sungold' mainly accumulates more sucrose and less citric acid and starch for the second flavor; and 'F43' mainly accumulates more titratable acid, citric acid, and starch for a lesser degree of sweetness. We investigated the DEGs associated with the starch and sucrose metabolism pathways, citrate cycle pathway, glycolysis pathway, and a handful of sugar transporter proteins, which were considered to be important regulators of sugar and acid accumulation. Additionally, an analysis of the co-expression network of weighted genes unveiled a robust correlation between the brown module and sucrose, glucose, and fructose, with VIP being identified as a hub gene that interacted with four sugar transporter proteins (SLC35B3, SLC32A, SLC2A8, and SLC2A13), as well as three structural genes for sugar and acid metabolism (MUR3, E3.2.1.67, and CSLD). Furthermore, we found some lncRNAs and miRNAs that regulate these genes. Our findings provide clues to the functional genes related to sugar metabolism, and lay the foundation for the selection and cultivation of high-sugar apricots in the future.

Keywords: WGCNA; acid; apricot; fruits; metabolome; sugar; transcriptome.

Figure 1

Changes in soluble sugar and organic acid contents at different developmental stages of apricot. (A) Phenotype of three apricots. (B–H) The contents of sucrose (B), glucose (C), fructose (D), sorbitol (E), citric acid (F), malate (G), and starch (H).

Figure 2

Gene expression and correlation between the transcriptomes of three representative stages each of three apricot cultivars. (A) The proportion of expressed genes in three apricot cultivars of three typical stages. (B) The proportion of expressed genes at four different expression levels in ‘Shushanggan’ (SS1−3), ‘Sungold’ (SJ1−3), and ‘F43’ (SF1−3). (C) Pearson correlation coefficient (PCC) of expressed genes from three representative stages in ‘Shushanggan’, ‘Sungold’, and ‘F43’. (D) Principal component analysis (PCA) plot showing clustering of transcriptomes of three representative stages in ‘Shushanggan’, ‘Sungold’, and ‘F43’.

Figure 3

Identification of candidate genes correlated with sugar and acid metabolism in ‘Shushanggan’, ‘Sungold’, and ‘F43’ fruits. (A) SSU, SJU, SFU: genes upregulated in ‘Shushanggan’, ‘Sungold’, and ‘F43’, respectively. (B) SSD, SJD, SFD: genes downregulated in ‘Shushanggan’, ‘Sungold’, and ‘F43’, respectively.

Figure 4

Expression patterns of DEGs involved in sugar and acid metabolic pathway. E2.4.1.14, sucrose-phosphate synthase; SPP, sucrose-6-phosphatase; ScrA, sucrose PTS system EIIBCA or EIIBC component; INV, beta-fructofuranosidase; SORD, L-iditol 2-dehydrogenase; ScrK, fructokinase; HK, hexokinase; GPI, glucose-6-phosphate isomerase; GCK, glucokinase; G6PC, glucose-6-phosphatase; SUS, sucrose synthase; UGP2, UTP-glucose-1-phosphate uridylyltransferase; ENPP1_3, ectonucleotide pyrophosphatase family member 1/3; glgC, glucose-1-phosphate adenylyltransferase; NUDX14, ADP-sugar diphosphatase; glgA, starch synthase; WAXY, granule-bound starch synthase; GBE1, 1,4-alpha-glucan branching enzyme; AMY, alpha-amylase; amyM, maltogenic alpha-amylase; MGAM, maltase−glucoamylase; SI, sucrase-isomaltase; E3.2.1.2, beta-amylase; pgm, phosphoglucomutase; PFK9, 6-phosphofructokinase; pfkC, ADP-dependent phosphofructokinase/glucokinase; ALDO, fructose-bisphosphate aldolase, class I; GADPH, glyceraldehyde 3-phosphate dehydrogenase; gap2, glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating); PGK, phosphoglycerate kinase; PGAM, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase; ENO, enolase; gpmI, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; PK, pyruvate kinase; PC, pyruvate carboxylase; ACLY, ATP citrate (pro−S)-lyase; CS, citrate synthase; MDH1, malate dehydrogenase.

Figure 5

Identification of hub genes in co-expression network. (A) Hierarchical clustering tree (cluster dendrogram) illustrating 13 modules of co-expressed genes pursuant to WGCNA. The same color indicates that the corresponding gene on the clustering tree belongs to the same module. (B) heatmap of module−sugar and acid relationships. Each row represents a module indicated by different colors. The color key from blue to red represents correlation values from −1 to 1. (C) MEbrown module gene expression patterns. (D) The co-expression network contained 52 co-expression genes for the MEbrown module.

Figure 6

Interaction networks of differential expression of sugar accumulation genes with lncRNAs and miRNAs. Yellow, blue, and red circles indicate mRNA, lncRNA, and miRNA, respectively.

Figure 7

Expression levels of 9 candidate DEGs validated via qRT−PCR. Columns and lines indicate RNA−seq and qRT−PCR of the candidate DEGs, respectively. Pearson correlation coefficients were calculated between qRT−PCR and RNA−Seq data of candidate DEGs. UBQ was used as the internal control. Error bars indicate SD.