Skip to main content
SpringerLink
Log in

A co-expression gene network associated with developmental regulation of apple fruit acidity

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Apple fruit acidity, which affects the fruit’s overall taste and flavor to a large extent, is primarily determined by the concentration of malic acid. Previous studies demonstrated that the major QTL malic acid (Ma) on chromosome 16 is largely responsible for fruit acidity variations in apple. Recent advances suggested that a natural mutation that gives rise to a premature stop codon in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) is the genetic causal element underlying Ma. However, the natural mutation does not explain the developmental changes of fruit malate levels in a given genotype. Using RNA-seq data from the fruit of ‘Golden Delicious’ taken at 14 developmental stages from 1 week after full-bloom (WAF01) to harvest (WAF20), we characterized their transcriptomes in groups of high (12.2 ± 1.6 mg/g fw, WAF03–WAF08), mid (7.4 ± 0.5 mg/g fw, WAF01–WAF02 and WAF10–WAF14) and low (5.4 ± 0.4 mg/g fw, WAF16–WAF20) malate concentrations. Detailed analyses showed that a set of 3,066 genes (including Ma1) were expressed not only differentially (P FDR < 0.05) between the high and low malate groups (or between the early and late developmental stages) but also in significant (P < 0.05) correlation with malate concentrations. The 3,066 genes fell in 648 MapMan (sub-) bins or functional classes, and 19 of them were significantly (P FDR < 0.05) co-enriched or co-suppressed in a malate dependent manner. Network inferring using the 363 genes encompassed in the 19 (sub-) bins, identified a major co-expression network of 239 genes. Since the 239 genes were also differentially expressed between the early (WAF03–WAF08) and late (WAF16–WAF20) developmental stages, the major network was considered to be associated with developmental regulation of apple fruit acidity in ‘Golden Delicious’.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Angeli A, Baetz U, Francisco R, Zhang J, Chaves M, Regalado A (2013) The vacuolar channel VvALMT9 mediates malate and tartrate accumulation in berries of Vitis vinifera. Planta 238:283–291

    Article  PubMed  Google Scholar 

  • Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48:381–390

    Article  CAS  PubMed  Google Scholar 

  • Assenov Y, Ramírez F, Schelhorn S-E, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282–284

    Article  CAS  PubMed  Google Scholar 

  • Baggerly KA, Deng L, Morris JS, Aldaz CM (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19:1477–1483

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, Dougherty L, Li M, Fazio G, Cheng L, Xu K (2012) A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple. Mol Genet Genomics 287:663–678

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, Dougherty L, Xu K (2014) Towards an improved apple reference transcriptome using RNA-seq. Mol Genet Genomics 289:427–438

    Article  CAS  PubMed  Google Scholar 

  • Barbier-Brygoo H, De Angeli A, Filleur S, Frachisse J-M, Gambale F, Thomine S, Wege S (2011) Anion channels/transporters in plants: from molecular bases to regulatory networks. Annu Rev Plant Biol 62:25–51

    Article  CAS  PubMed  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc Ser B-Methodol 57:289–300

    Google Scholar 

  • Beruter J (2004) Carbohydrate metabolism in two apple genotypes that differ in malate accumulation. J Plant Physiol 161:1011–1029

    Article  PubMed  Google Scholar 

  • Blanke MM, Lenz F (1989) Fruit photosynthesis. Plant Cell Environ 12:31–46

    Article  CAS  Google Scholar 

  • Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang P-L, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366–2382

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Collins NC, Shirley NJ, Saeed M, Pallotta M, Gustafson JP (2008) An ALMT1 gene cluster controlling aluminum tolerance at the Alt4 locus of rye (Secale cereale L.). Genetics 179:669–682

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Delhaize E, Ma JF, Ryan PR (2012) Transcriptional regulation of aluminium tolerance genes. Trends Plant Sci 17:341–348

    Article  CAS  PubMed  Google Scholar 

  • Emmerlich V, Linka N, Reinhold T, Hurth MA, Traub M, Martinoia E, Neuhaus HE (2003) The plant homolog to the human sodium/dicarboxylic cotransporter is the vacuolar malate carrier. P Natl Acad Sci USA 100:11122–11126

    Article  CAS  Google Scholar 

  • Eticha D, Stass A, Horst WJ (2005) Cell–wall pectin and its degree of methylation in the maize root–apex: significance for genotypic differences in aluminium resistance. Plant Cell Environ 28:1410–1420

    Article  CAS  Google Scholar 

  • Etienne A, Génard M, Lobit P, Mbeguié-A-Mbéguié D, Bugaud C (2013) What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells. J Exp Bot 64:1451–1469

    Article  CAS  PubMed  Google Scholar 

  • Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23:257–258

    Article  CAS  PubMed  Google Scholar 

  • Fernie AR, Carrari F, Sweetlove LJ (2004) Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport. Curr Opin Plant Biol 7:254–261

    Article  CAS  PubMed  Google Scholar 

  • Gasic K, Hernandez A, Korban SS (2004) RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA library construction. Plant Mol Biol Rep 22:437–438

    Article  CAS  Google Scholar 

  • Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435

    Article  PubMed Central  PubMed  Google Scholar 

  • Gowik U, Bräutigam A, Weber KL, Weber APM, Westhoff P (2011) Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? Plant Cell 23:2087–2105

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gutierres S, Sabar M, Lelandais C, Chetrit P, Diolez P, Degand H, Boutry M, Vedel F, de Kouchkovsky Y, De Paepe R (1997) Lack of mitochondrial and nuclear-encoded subunits of complex I and alteration of the respiratory chain in Nicotiana sylvestris mitochondrial deletion mutants. P Natl Acad Sci USA 94:3436–3441

    Article  CAS  Google Scholar 

  • Hoekenga OA, Maron LG, Pineros MA, Cancado GMA, Shaff J, Kobayashi Y, Ryan PR, Dong B, Delhaize E, Sasaki T, Matsumoto H, Yamamoto Y, Koyama H, Kochian LV (2006) AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis. P Natl Acad Sci USA 103:9738–9743

    Article  CAS  Google Scholar 

  • Hu L, Sun H, Li R, Zhang L, Wang S, Sui X, Zhang Z (2011) Phloem unloading follows an extensive apoplasmic pathway in cucumber (Cucumis sativus L.) fruit from anthesis to marketable maturing stage. Plant Cell Environ 34:1835–1848

    Article  CAS  PubMed  Google Scholar 

  • Hulme AC, Wooltorton LSC (1957) The organic acid metabolism of apple fruits: changes in individual acids during growth on the tree. J Sci Food Agr 8:117–122

    Article  CAS  Google Scholar 

  • Jung S, Ficklin SP, Lee T, Cheng C-H, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D (2014) The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Res 42:D1237–D1244

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z (2013) Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell 25:1960–1978

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Keller M, Shrestha P (2014) Solute accumulation differs in the vacuoles and apoplast of ripening grape berries. Planta 239:633–642

    Article  CAS  PubMed  Google Scholar 

  • Kenis K, Keulemans J, Davey M (2008) Identification and stability of QTLs for fruit quality traits in apple. Tree Genet Genomes 4:647–661

    Article  Google Scholar 

  • Khan S, Beekwilder J, Schaart J, Mumm R, Soriano J, Jacobsen E, Schouten H (2013) Differences in acidity of apples are probably mainly caused by a malic acid transporter gene on LG16. Tree Genet Genomes 9:475–487

    Article  Google Scholar 

  • Klie S, Nikoloski Z (2012) The choice between mapman and gene ontology for automated gene function prediction in plant science. Front Genet 3:1–14

    Article  Google Scholar 

  • Kovermann P, Meyer S, Hortensteiner S, Picco C, Scholz-Starke J, Ravera S, Lee Y, Martinoia E (2007) The Arabidopsis vacuolar malate channel is a member of the ALMT family. Plant J 52:1169–1180

    Article  CAS  PubMed  Google Scholar 

  • Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C (2003) Mapping quantitative physiological traits in apple (Malus x domestica Borkh.). Plant Mol Biol 52:511–526

    Article  CAS  PubMed  Google Scholar 

  • Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR (2006) Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Protoc 1:387–396

    Article  CAS  PubMed  Google Scholar 

  • Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B (2014) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ 37:1250–1258

    Article  CAS  PubMed  Google Scholar 

  • Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, den Nijs APM, Periam N, Rikkerink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, Verhaegh JJ, Vrielink-van Ginkel M, King GJ (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73

    Article  CAS  Google Scholar 

  • Meyer S, Scholz-Starke J, De Angeli A, Kovermann P, Burla B, Gambale F, Martinoia E (2011) Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation. Plant J 67:247–257

    Article  CAS  PubMed  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  PubMed  Google Scholar 

  • Nelson DL, Lehninger AL, Cox MM (2008) Pathways of Amino Acid Degradation. Lehninger principles of biochemistry, 5th edn. W.H. Freeman, New York, pp 687-706

  • Noctor G, Dutilleul C, De Paepe R, Foyer CH (2004) Use of mitochondrial electron transport mutants to evaluate the effects of redox state on photosynthesis, stress tolerance and the integration of carbon/nitrogen metabolism. J Exp Bot 55:49–57

    Article  CAS  PubMed  Google Scholar 

  • Osorio S, Vallarino JG, Szecowka M, Ufaz S, Tzin V, Angelovici R, Galili G, Fernie AR (2013) Alteration of the Interconversion of pyruvate and malate in the plastid or cytosol of ripening tomato fruit invokes diverse consequences on sugar but similar effects on cellular organic acid, metabolism, and transitory starch accumulation. Plant Physiol 161:628–643

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ruan Y, Mate C, Patrick J, Brady C (1995) Non-destructive collection of apoplast fluid from developing tomato fruit using a pressure dehydration procedure. Funct Plant Biol 22:761–769

    Google Scholar 

  • Saeed A, Bhagabati N, Braisted J, Liang W, Sharov V, Howe E, Li J, Thiagarajan M, White J, Quackenbush J (2006) TM4 microarray software suite. Methods Enzymol 411:134–193

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Yamamoto Y, Ezaki B, Katsuhara M, Ahn SJ, Ryan PR, Delhaize E, Matsumoto H (2004) A wheat gene encoding an aluminum-activated malate transporter. Plant J 37:645–653

    Article  CAS  PubMed  Google Scholar 

  • Schumacher K, Krebs M (2010) The V-ATPase: small cargo, large effects. Curr Opin Plant Biol 13:724–730

    Article  CAS  PubMed  Google Scholar 

  • Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J (2013) Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. Plant Cell 25:4285–4304

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Smith E, Naik D, Cumming JR (2011) Genotypic variation in aluminum resistance, cellular aluminum fractions, callose and pectin formation and organic acid accumulation in roots of Populus hybrids. Environ Exp Bot 72:182–193

    Article  CAS  Google Scholar 

  • Sweetman C, Deluc LG, Cramer GR, Ford CM, Soole KL (2009) Regulation of malate metabolism in grape berry and other developing fruits. Phytochemistry 70:1329–1344

    Article  CAS  PubMed  Google Scholar 

  • Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939

    Article  CAS  PubMed  Google Scholar 

  • Ulrich R (1970) Organic acids. In: Hulme A (ed) The biochemistry of fruit and their products. Academic Press, London and New York, pp 89–118

    Google Scholar 

  • Usadel B, Nagel A, Steinhauser D, Gibon Y, Blasing O, Redestig H, Sreenivasulu N, Krall L, Hannah M, Poree F, Fernie A, Stitt M (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7:535

    Article  PubMed Central  PubMed  Google Scholar 

  • Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32:1211–1229

    Article  PubMed  Google Scholar 

  • Wang A, Xu K (2012) Characterization of two orthologs of reversion-to-ethylene sensitivity1 in apple. J Mol Biol Res 2:24–41

    Article  Google Scholar 

  • Wehr JB, Menzies NW, Blamey FPC (2003) Model studies on the role of citrate, malate and pectin esterification on the enzymatic degradation of Al- and Ca-pectate gels: possible implications for Al-tolerance. Plant Physiol Bioch 41:1007–1010

    Article  CAS  Google Scholar 

  • Wheeler MCG, Tronconi MA, Drincovich MF, Andreo CS, Flügge U-I, Maurino VG (2005) A comprehensive analysis of the nadp-malic enzyme gene family of Arabidopsis. Plant Physiol 139:39–51

    Article  CAS  PubMed  Google Scholar 

  • Wilcoxon F (1945) Individual comparisons by ranking methods. Biometrics 1:80–83

    Article  Google Scholar 

  • Wong D, Sweetman C, Drew D, Ford C (2013) VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine). BMC Genom 14:882

    Article  Google Scholar 

  • Xu K, Wang A, Brown S (2012) Genetic characterization of the Ma locus with pH and titratable acidity in apple. Mol Breeding 30:899–912

    Article  CAS  Google Scholar 

  • Yamaji N, Huang CF, Nagao S, Yano M, Sato Y, Nagamura Y, Ma JF (2009) A zinc finger transcription factor art1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21:3339–3349

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yang XY, Zeng ZH, Yan JY, Fan W, Bian HW, Zhu MY, Yang JL, Zheng SJ (2013) Association of specific pectin methylesterases with Al-induced root elongation inhibition in rice. Physiol Plantarum 148:502–511

    Article  CAS  Google Scholar 

  • Yao YX, Li M, Liu Z, You CX, Wang DM, Zhai H, Hao YJ (2009) Molecular cloning of three malic acid related genes MdPEPC, MdVHA-A, MdcyME and their expression analysis in apple fruits. Sci Hortic 122:404–408

    Article  CAS  Google Scholar 

  • Yao Y-X, Li M, Zhai H, You C-X, Hao Y-J (2011) Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis. J Plant Physiol 168:474–480

    Article  CAS  PubMed  Google Scholar 

  • Zhang LY, Peng YB, Pelleschi-Travier S, Fan Y, Lu YF, Lu YM, Gao XP, Shen YY, Delrot S, Zhang DP (2004) Evidence for apoplasmic phloem unloading in developing apple fruit. Plant Physiol 135:574–586

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang XY, Wang XL, Wang XF, Xia GH, Pan QH, Fan RC, Wu FQ, Yu XC, Zhang DP (2006) A shift of phloem unloading from symplasmic to apoplasmic pathway is involved in developmental onset of ripening in grape berry. Plant Physiol 142:220–232

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang YZ, Li PM, Cheng LL (2010) Developmental changes of carbohydrates, organic acids, amino acids, and phenolic compounds in ‘Honeycrisp’ apple flesh. Food Chem 123:1013–1018

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We thank Dr. Zhangjun Fei and Dr. Yi Zheng for their helpful comments on the RNA seq data analysis. We also thank Drs Doreen Main and Stephen Ficklin for formatting the revised apple reference transcriptome and making it publically available through the Genome Database for Rosaceae (GDR). This work was supported in part by the Agriculture and Food Research Initiative competitive grant no. 2014-67013-21660 of the USDA National Institute of Food and Agriculture.

Author information

Authors and Affiliations

  1. Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, USA

    Yang Bai, Laura Dougherty & Kenong Xu

  2. Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Lailiang Cheng

Authors
  1. Yang Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laura Dougherty
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lailiang Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kenong Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kenong Xu.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (Docx 173 kb)

Supplementary material 2 (Xlsx 591 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bai, Y., Dougherty, L., Cheng, L. et al. A co-expression gene network associated with developmental regulation of apple fruit acidity. Mol Genet Genomics 290, 1247–1263 (2015). https://doi.org/10.1007/s00438-014-0986-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-014-0986-2

Keywords

Search

Navigation