Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder.
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.
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
Ana M
AM
Ibáñez
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA; Department of Agricultural and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy; I.E.M.E.S.T. Istituto Euro Mediterraneo di Scienza e Tecnologia, Via Emerico Amari, 123, 90139 Palermo, Italy.
Federico
F
Martinelli
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
Russell L
RL
Reagan
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
Sandra L
SL
Uratsu
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
Anna
A
Vo
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
Mario A
MA
Tinoco
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
My L
ML
Phu
Division of Biostatistics, Med Sci 1C, Room 146, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
Ying
Y
Chen
Division of Biostatistics, Med Sci 1C, Room 146, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
David M
DM
Rocke
Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA. Electronic address: amdandekar@ucdavis.edu.
Abhaya M
AM
Dandekar
D002957:Citrus / Q000235:genetics* / Q000378:metabolism*; D005638:Fruit / Q000378:metabolism*; D020869:Gene Expression Profiling; D055432:Metabolomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D060066:Protein Interaction Maps; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D010937:Plant Growth Regulators; D014157:Transcription Factors
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