Article

The PH gene determines fruit acidity and contributes to the evolution of sweet melons

  • Nature Communications 5, Article number: 4026 (2014)
  • doi:10.1038/ncomms5026
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Abstract

Taste has been the subject of human selection in the evolution of agricultural crops, and acidity is one of the three major components of fleshy fruit taste, together with sugars and volatile flavour compounds. We identify a family of plant-specific genes with a major effect on fruit acidity by map-based cloning of C. melo PH gene (CmPH) from melon, Cucumis melo taking advantage of the novel natural genetic variation for both high and low fruit acidity in this species. Functional silencing of orthologous PH genes in two distantly related plant families, cucumber and tomato, produced low-acid, bland tasting fruit, showing that PH genes control fruit acidity across plant families. A four amino-acid duplication in CmPH distinguishes between primitive acidic varieties and modern dessert melons. This fortuitous mutation served as a preadaptive antecedent to the development of sweet melon cultigens in Central Asia over 1,000 years ago.

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References

  1. 1.

    , & Sugar, acid, and flavor in fresh fruits. J. Am. Dietetic Assoc. 57, 432–435 (1970).

  2. 2.

    inThe Biochemistry of Fruits and Their Products (ed. Hulme A. C. 89–117Academic Press (1970).

  3. 3.

    et al. Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.). Theor. App. Gen. 125, 343–353 (2012).

  4. 4.

    , & Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome 40, 841–849 (1997).

  5. 5.

    et al. Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor. App. Gen. 105, 145–159 (2002).

  6. 6.

    et al. 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 (2012).

  7. 7.

    et al. What controls fruit acidity? A review of malate and citrate accumulation in fruit cells. J. Exp. Bot. 64, 1451–1469 (2013).

  8. 8.

    , , , & Colour-enhancing protein in blue petals. Nature 407, 581 (2000).

  9. 9.

    et al. An H+ P-ATPase on the tonoplast determines vacuolar pH and flower colour. Nat. Cell Biol. 10, 1456–1462 (2008).

  10. 10.

    , & Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 10, 236–242 (2005).

  11. 11.

    et al. Hyperacidification of vacuoles by the combined action of two different P-ATPases in the tonoplast determines flower color. Cell Rep. 6, 32–43 (2014).

  12. 12.

    et al. Some comments on infraspecific classification of cultivars of melon. In Proceedings of Cucurbitaceae 2000 (eds Katzir N. Paris H. S.) ISHS, Belgium. Acta Hort. 510, 29–36 (2000).

  13. 13.

    et al. Genetic diversity of Cucumis melo. Hort. Rev. 36, 165–198 (2009).

  14. 14.

    Inheritance of some characters in muskmelons (Cucumis melo). Genet. Polonica 3, 265–274 (1962).

  15. 15.

    et al. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theor. App. Gen. 121, 511–533 (2010).

  16. 16.

    et al. Development of sweet melon (Cucumis melo) genotypes combining high sucrose and organic acid content. J. Am. Soc. Hortic. Sci. 128, 537–540 (2003).

  17. 17.

    et al. The genome of melon (Cucumis melo L.). Proc. Natl Acad. Sci. USA 109, 11872–11877 (2012).

  18. 18.

    , & Malic and citric acids in pickling cucumbers. J. Food Sci. 47, 1859–1861 1865 (1982).

  19. 19.

    et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature 485, 119–122 (2012).

  20. 20.

    et al. Evolution and structural diversification of PILS putative auxin carriers in plants. Front. Plant Sci. 3, 227 (2012).

  21. 21.

    , & Sensors and regulators of intracellular pH. Nat. Rev. Mol. Cell Biol. 11, 50–61 (2010).

  22. 22.

    et al. Identification of a novel adenine nucleotide transporter in the endoplasmic reticulum of Arabidopsis. Plant Cell 20, 438–451 (2008).

  23. 23.

    et al. A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321, 836–838 (2008).

  24. 24.

    , , & Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc. Natl Acad. Sci. USA 107, 14269–14273 (2010).

  25. 25.

    et al. inGenetics, Genomics and Breeding of Crop Plants (eds Wang Y. H.et al. 140–198CRC Press (2012).

  26. 26.

    , & The cucurbits of mediterranean antiquity: identification of taxa from ancient images and descriptions. Ann. Botany 100, 1441–1457 (2007).

  27. 27.

    Historical records, origins, and development of the edible cultivar groups of Cucurbita pepo (Cucurbitaceae). Econ. Bot. 43, 423–443 (1989).

  28. 28.

    , & Medieval emergence of sweet melons, Cucumis melo (Cucurbitaceae). Ann. Botany 110, 23–33 (2012).

  29. 29.

    & The nature of selection during plant domestication. Nature 457, 843–848 (2009).

  30. 30.

    et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).

  31. 31.

    , & Rice domestication by reducing shattering. Science 311, 1936–1939 (2006).

  32. 32.

    et al. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 173, 975–983 (2006).

  33. 33.

    Syngenta Participation AG. Novel Melon Plants. European Union patent, EP1587933 (2008).

  34. 34.

    & Sucrose phosphate synthase, sucrose synthase, and invertase activities in developing fruit of Lycopersicon esculentum Mill. and the sucrose-accumulating L. hirsutum Humb. and Bonpl. Plant Physiol. 95, 623–627 (1991).

  35. 35.

    et al. The TYLCV-tolerant tomato line MP-1 is characterized by superior transformation competence. J. Exp. Bot. 48, 1919–1923 (1997).

  36. 36.

    et al. Transgenic cucumbers harboring the 54-kDa putative gene of cucumber fruit mottle mosaic tobamovirus are highly resistant to viral infection and protect non-transgenic scions from soil infection. Transgenic Res. 14, 81–93 (2005).

  37. 37.

    , , & Plant Genetic Transformation And Gene Expression: A Laboratory Manual Blackwell Scientific (1988).

  38. 38.

    , , , & The identification of a gene (Cwp1), silenced during Solanum evolution, which causes cuticle microfissuring and dehydration when expressed in tomato fruit. Plant J. 52, 627–639 (2007).

  39. 39.

    et al. High-throughput marker discovery in melon using a self-designed oligo microarray. BMC Genomics 11, 269 (2010).

  40. 40.

    et al. Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon. Theor. Appl. Genet. 126, 349–358 (2013).

  41. 41.

    et al. Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581–590 (2001).

  42. 42.

    et al. pSAT vectors: a modular series of plasmids for fluorescent protein tagging and expression of multiple genes in plants. Plant Mol. Biol. 57, 503–516 (2005).

  43. 43.

    et al. A comparative study of the involvement of 17 Arabidopsis myosin family members on the motility of Golgi and other organelles. Plant Physiol. 150, 700–709 (2009).

  44. 44.

    , , & An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J. 33, 949–956 (2003).

  45. 45.

    , , & Agroinjection of tomato fruits. A tool for rapid functional analysis of transgenes directly in fruit. Plant Physiol. 140, 3–11 (2006).

  46. 46.

    et al. Purification and functional characterization of protoplasts and intact vacuoles from grape cells. BMC Res. Notes 3, 19 (2010).

  47. 47.

    , , & Characterization of a concentrative type of adenosine transporter from Arabidopsis thaliana (ENT1,At). FEBS Lett. 509, 370–374 (2001).

  48. 48.

    et al. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harb. Protoc. 2011, 940–949 (2011).

  49. 49.

    , , & Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

  50. 50.

    , & TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

  51. 51.

    & Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 35–37 (2007).

  52. 52.

    , & SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221–224 (2010).

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Acknowledgements

We are grateful to J. Garcia-Mas for prepublication access to the melon genome sequence, to Dr Einat Sadot and Dr Mohammed Abu-Abied for assistance with the organellar markers and to Dr Amit Gal-On for assistance with cucumber transgenics. We gratefully acknowledge financial support from the Chief Scientist, Ministry of Agriculture; The Israel Bio-Tov Consortium & Magnet Program, Israel Ministry of Industry, Trade and Labour; Binational Agriculture Research and Development (BARD) Grants IS-3877-06 and IS-4223-09C; Israel Science Foundation Grant No. 386/06 and EU project Food-2005 MetaPhor. Melon RIL lines are available upon request from N.K. and melon near-isogenic lines are available upon request from Y.B.

Author information

Author notes

    • Shahar Cohen
    •  & Maxim Itkin

    These authors contributed equally to this work

Affiliations

  1. Department of Vegetable Research, ARO-Volcani Center, Bet Dagan 50250, Israel

    • Shahar Cohen
    • , Maxim Itkin
    • , Yelena Yeselson
    • , Dalia Wolf
    • , Marina Petreikov
    • , Shmuel Shen
    •  & Arthur A. Schaffer
  2. Department of Vegetable Research, ARO-Newe Ya‘ar Center, Ramat Yishay 30095, Israel

    • Galil Tzuri
    • , Vitaly Portnoy
    • , Rotem Harel-Baja
    • , Shery Lev
    • , Uzi Sa‘ar
    • , Rachel Davidovitz-Rikanati
    • , Nadine Baranes
    • , Einat Bar
    • , Efraim Lewinsohn
    • , Yaakov Tadmor
    • , Harry S. Paris
    • , Nurit Katzir
    •  & Yosef Burger
  3. Department of Biological Services, Weizmann Institute, Rehovot 76100, Israel

    • Shifra Ben-Dor
  4. Department of Plant Sciences, Weizmann Institute, Rehovot 76100, Israel

    • Ilana Rogachev
    •  & Asaph Aharoni
  5. Department of Biochemistry, Weizmann Institute, Rehovot 76100, Israel

    • Tslil Ast
    •  & Maya Schuldiner
  6. Department of Fruit Tree Research, ARO-Volcani Center, Bet Dagan 50250, Israel

    • Eduard Belausov
    • , Ravit Eshed
    • , Ron Ophir
    •  & Amir Sherman
  7. Department of Pflanzenphysiologie, Technische Universitat Kaiserlautern, D-67663 Kaiserlautern, Germany

    • Benedikt Frei
    •  & H. Ekkehard Neuhaus
  8. Boyce Thompson Institute for Plant Science, Ithaca, New York 14853, USA

    • Yimin Xu
    • , Zhangjun Fei
    •  & Jim Giovannoni

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Contributions

The project was designed by A.A.S., Y.B., N.K., H.S.P., Y.T. and E.L; S.C, M.I., Y.Y., G.T., V.P., R.H.-B., S.L., R.D.-R., N.B., E.B., M.P., S.S., R.E., R.O. and A.S. carried out the mapping, cloning and gene identification; Y.B., N.K., G.T., V.P., R.H.-B., S.L., U.S. and S.S. were responsible for the development of the plant genetic material; metabolomics analyses were performed by M.I., Y.Y., M.P., I.R. and A.A.; preparation of transgenic plants and yeast lines was carried out by S.C., D.W., R.D.-R., N.B., T.A. and M.S.; bioinformatic and genomic analyses were performed by M.I., S.B.-D., N.K., S.L., V.P., G.T., Y.X., Z.F. and J.G.; metabolite uptake and efflux experiments were performed by S.C., M.I., M.P., Y.Y., B.F. and H.E.N.; E.B., T.A. and M.S. were responsible for the microscopy. A.A.S. and H.S.P. co-wrote the manuscript. S.C. and M.I. contributed equally to the research.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Arthur A. Schaffer.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures, Tables, Methods and References

    Supplementary Figures 1-9, Supplementary Tables 1-3, Supplementary Methods and Supplementary References

Excel files

  1. 1.

    Supplementary Data 1

    Transmembrane Prediction for the PH gene.

  2. 2.

    Supplementary Data 2

    Substances, significantly changed in at least one of the developmental stages of melon fruit.

  3. 3.

    Supplementary Data 3

    Substances, significantly different between wild type and RNAi of ripe cucumber fruit.

  4. 4.

    Supplementary Data 4

    Substances, significantly changed between wild type and RNAi plants in at least one of the developmental stages of tomato fruit.

  5. 5.

    Supplementary Data 5

    Tomato, melon and cucumber share similar m/z values.

  6. 6.

    Supplementary Data 6

    Description of varieties of melon used in this study.

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