Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder

Abstract

A systems-level analysis reveals details of molecular mechanisms underlying puffing disorder in Citrus fruit. Flavedo, albedo and juice sac tissues of normal fruits and fruits displaying symptoms of puffing disorder were studied using metabolomics at three developmental stages. Microarrays were used to compare normal and puffed fruits for each of the three tissues. A protein-protein interaction network inferred from previous work on Arabidopsis identified hub proteins whose transcripts show significant changes in expression. Glycolysis, the backbone of primary metabolism, appeared to be severely affected by the disorder, based on both transcriptomic and metabolomic results. Significantly less citric acid was observed consistently in puffed fruits. Gene set enrichment analysis suggested that glycolysis and carbohydrate metabolism were significantly altered in puffed samples in both albedo and flavedo. Expression of invertases and genes for sucrose export, amylose-starch and starch-maltose conversion was higher in puffed fruits. These changes may significantly alter source-sink communications. Genes associated with gibberellin and cytokinin signaling were downregulated in symptomatic albedo tissues, suggesting that these hormones play key roles in the disorder. Findings may be applied toward the development of early diagnostic methods based on host response genes and metabolites (i.e. citric acid), and toward therapeutics based on hormones.

Keywords: ABA; APG6; Albedo breakdown; BA; CDC2; CHO; Citrus; FDR; FPS2; Fruit disorder; GA; GABA; GASA; GAs; GC–MS; GSEA; HB; HSP; IAA; Metabolomics; NADH; PEP; PPDK; PPI; Puffing; SA; TCA; TF; Transcriptomics; abscisic acid; albino pale green 6; brassinosteroid; carbohydrate; cell division control 2; false discovery rate; farnesyl diphosphate synthase 2; gas chromatography–mass spectrometry; gene set enrichment analysis; gibberelic acid; gibberelins; gibberellin-responsive protein 4; heat shock proteins; homeobox; indole-3-acetic acid; nicotinamide adenine dinucleotide (reduced form); phosphoenolpyruvate; protein–protein interactions; pyruvate orthophosphate dikinase; salicylic acid; transcription factor; tricarboxylic acid; γ-aminobutyric acid.