Abstract
Main conclusion
Transcriptome analysis of a persimmon population segregating for an astringency trait in fruit suggested central roles for a limited number of transcriptional regulators in the loss of proanthocyanidin accumulation.
Persimmon (Diospyros kaki; 2n = 6x = 90) accumulates a large amount of proanthocyanidins (PAs) in its fruit, resulting in an astringent taste. Persimmon cultivars are classified into four types based on the nature of astringency loss and the amount of PAs at maturity. Pollination constant and non-astringent (PCNA)-type cultivars stop accumulating PAs in the early stages of fruit development and their fruit can be consumed when still firm without the need for artificial deastringency treatments. While the PCNA trait has been shown to be conferred by a recessive allele at a single locus (ASTRINGENCY; AST), the exact genetic determinant remains unidentified. Here, we conducted transcriptome analyses to elucidate the regulatory mechanism underlying this trait using developing fruits of an F1 population segregating for the PCNA trait. Comparisons of the transcriptomes of PCNA and non-PCNA individuals and hierarchical clustering revealed that genes related to the flavonoid pathway and to abiotic stress responses involving light stimulation were expressed coordinately with PA accumulation. Furthermore, coexpression network analyses suggested that three putative transcription factors were central to the PA regulatory network and that at least DkMYB4 and/or DkMYC1, which have been reported to form a protein complex with each other for PA regulation, may have a central role in the differential expression of PA biosynthetic pathway genes between PCNA and non-PCNA.
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Abbreviations
- AST :
-
ASTRINGENCY
- CIPK:
-
CBL-interacting protein kinase
- GO:
-
Gene ontology
- PA:
-
Proanthocyanidin
- PCNA:
-
Pollination constant and non-astringent
- RPKM:
-
Reads per kilobase of exon per million reads
References
Akagi T, Ikegami A, Suzuki Y, Yoshida J, Yamada M, Sato A, Yonemori K (2009a) Expression balances of structural genes in shikimate and flavonoid biosynthesis cause a difference in proanthocyanidin accumulation in persimmon (Diospyros kaki Thunb.) fruit. Planta 230:899–915. https://doi.org/10.1007/s00425-009-0991-6
Akagi T, Ikegami A, Tsujimoto T, Kobayashi S, Sato A, Kono A, Yonemori K (2009b) DkMyb4 is a Myb transcription factor involved in proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol 151:2028–2045. https://doi.org/10.1104/pp.109.146985
Akagi T, Ikegami A, Yonemori K (2010) DkMyb2 wound-induced transcription factor of persimmon (Diospyros kaki Thunb.), contributes to proanthocyanidin regulation. Planta 232:1045–1059. https://doi.org/10.1007/s00425-010-1241-7
Akagi T, Katayama-Ikegami A, Yonemori K (2011) Proanthocyanidin biosynthesis of persimmon (Diospyros kaki Thunb.) fruit. Sci Hortic 130:373–380. https://doi.org/10.1016/j.scienta.2011.07.021
Akagi T, Katayama-Ikegami A, Kobayashi S, Sato A, Kono A, Yonemori K (2012a) Seasonal abscisic acid signal and a basic leucine zipper transcription factor, DkbZIP5, regulate proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol 158:1089–1102. https://doi.org/10.1104/pp.111.191205
Akagi T, Tao R, Tsujimoto T, Kono A, Yonemori K (2012b) Fine genotyping of a highly polymorphic ASTRINGENCY-linked locus reveals variable hexasomic inheritance in persimmon (Diospyros kaki Thunb.) cultivars. Tree Genet Genomes 8:195–204. https://doi.org/10.1007/s11295-011-0432-0
Akagi T, Henry IM, Tao R, Comai L (2014) A Y-chromosome-encoded small RNA acts as a sex determinant in persimmons. Science 346:646–650. https://doi.org/10.1126/science.1257225
Aron PM, Kennedy JA (2008) Flavan-3-ols: nature, occurrence and biological activity. Mol Nutr Food Res 52:79–104. https://doi.org/10.1002/mnfr.200700137
Bagchi D, Swaroop A, Preuss HG, Bagchi M (2014) Free radical scavenging, antioxidant and cancer chemoprevention by grape seed proanthocyanidin: an overview. Mutat Res 768:69–73. https://doi.org/10.1016/j.mrfmmm.2014.04.004
Berry JO, Yerramsetty P, Zielinski AM, Mure CM (2013) Photosynthetic gene expression in higher plants. Photosynth Res 117:91–120. https://doi.org/10.1007/s11120-013-9880-8
Collinge DB, Kragh KM, Mikkelsen JD, Nielsen KK, Rasmussen U, Vad K (1993) Plant chitinases. Plant J 3:31–40
del Mar Naval M, Gil-Muñoz F, Lloret A, Besada C, Salvador A, Badenes ML, Ríos G (2016) A WD40-repeat protein from persimmon interacts with the regulators of proanthocyanidin biosynthesis DkMYB2 and DkMYB4. Tree Genet Genomes 12:1–11. https://doi.org/10.1007/s11295-016-0969-z
Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins—a final frontier in flavonoid research? New Phytol 165:9–28. https://doi.org/10.1111/j.1469-8137.2004.01217.x
Edel KH, Kudla J (2016) Integration of calcium and ABA signaling. Curr Opin Plant Biol 33:83–91. https://doi.org/10.1016/j.pbi.2016.06.010
Epple P, Mack AA, Morris VR, Dangl JL (2003) Antagonistic control of oxidative stress-induced cell death in Arabidopsis by two related, plant-specific zinc finger proteins. Proc Natl Acad Sci USA 100:6831–6836. https://doi.org/10.1073/pnas.1130421100
Fini A, Brunetti C, Di Ferdinando M, Ferrini F, Tattini M (2011) Stress-induced flavonoid biosynthesis and the antioxidant machinery of plants. Plant Signal Behav 6:709–711. https://doi.org/10.4161/psb.6.5.15069
Herrmann KM, Weaver LM (1999) The shikimate pathway. Annu Rev Plant Physiol Plant Mol Biol 50:473–503. https://doi.org/10.1146/annurev.arplant.50.1.473
Hu Z, Mellor J, Wu J, DeLisi C (2004) VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinform 5:17. https://doi.org/10.1186/1471-2105-5-17
Ikeda I, Yamada M, Kurihara A, Nishida T (1985) Inheritance of astringency in Japanese persimmon. J Jpn Soc Hortic Sci 54:39–45
Ikegami A, Eguchi S, Kitajima A, Inoue K, Yonemori K (2007) Identification of genes involved in proanthocyanidin biosynthesis of persimmon (Diospyros kaki) fruit. Plant Sci 172:1037–1047. https://doi.org/10.1016/j.plantsci.2007.02.010
Jaakola L, Hohtola A (2010) Effect of latitude on flavonoid biosynthesis in plants. Plant Cell Environ 33:1239–1247. https://doi.org/10.1111/j.1365-3040.2010.02154.x
Kanzaki S, Akagi T, Masuko T, Kimura M, Yamada M, Sato A, Mitani N, Ustunomiya N, Yonemori K (2010) SCAR markers for practical application of marker-assisted selection in persimmon (Diospyros kaki Thunb.) breeding. J Jpn Soc Hortic Sci 79:150–155. https://doi.org/10.2503/jjshs1.79.150
Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinform 9:559. https://doi.org/10.1186/1471-2105-9-559
Lepiniec L, Debeaujon I, Routaboul J-M, Baudry A, Pourcel L, Nesi N, Caboche M (2006) Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol 57:405–430. https://doi.org/10.1146/annurev.arplant.57.032905.105252
Li S (2014) Transcriptional control of flavonoid biosynthesis: fine-tuning of the MYB-bHLH-WD40 (MBW) complex. Plant Signal Behav 8:1–7. https://doi.org/10.4161/psb.27522
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Li Y-G, Tanner G, Larkin P (1996) The DMACA-HCl protocol and the threshold proanthocyanidin content for bloat safety in forage legumes. J Sci Food Agric 70:89–101. https://doi.org/10.1002/(SICI)1097-0010(199601)70:1<89:AID-JSFA470>3.0.CO;2-N
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Nishiyama S, Yonemori K, Ueda J (2014) Effect of ABA treatment on tannin accumulation at an early stage of fruit development in persimmon. Acta Hortic 1042:217–222
Nishiyama S, Onoue N, Kono A, Sato A, Ushijima K, Yamane H, Tao R, Yonemori K (2017) Comparative mapping of the ASTRINGENCY locus controlling fruit astringency in hexaploid persimmon (Diospyros kaki Thunb.) with the diploid D. lotus reference genome. Hortic J (in press)
Pelloux J, Rustérucci C, Mellerowicz EJ (2007) New insights into pectin methylesterase structure and function. Trends Plant Sci 12:267–277. https://doi.org/10.1016/j.tplants.2007.04.001
Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR (2013) The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiol Biochem 72:21–34. https://doi.org/10.1016/j.plaphy.2013.02.001
Sato A, Yamada M (2016) Persimmon breeding in Japan for pollination-constant non-astringent (PCNA) type with marker-assisted selection. Breed Sci 66:60–68. https://doi.org/10.1270/jsbbs.66.60
Shi J, Kim KN, Ritz O, Albrecht V, Gupta R, Harter K, Luan S, Kudla J (1999) Novel protein kinases associated with calcineurin B-like calcium sensors in Arabidopsis. Plant Cell 11:2393–2405. https://doi.org/10.1105/tpc.11.12.2393
Su F, Hu J, Zhang Q, Luo Z (2012) Isolation and characterization of a basic helix-loop-helix transcription factor gene potentially involved in proanthocyanidin biosynthesis regulation in persimmon (Diospyros kaki Thunb.). Sci Hortic 136:115–121. https://doi.org/10.1016/j.scienta.2012.01.013
Taira S, Matsumto N, Ono M (1998) Accumulation of soluble and insoluble tannins during fruit development in nonastringent and astringent persimmon. J Jpn Soc Hortic Sci 67:572–576. https://doi.org/10.1248/cpb.37.3229
Terrier N, Torregrosa L, Ageorges A, Vialet S, Verries C, Cheynier V, Romieu C (2009) Ectopic expression of VvMybPA2 promotes proanthocyanidin biosynthesis in grapevine and suggest additional targets in the pathway. Plant Physiol 149:1028–1041. https://doi.org/10.1104/pp.108.131862
Wan CY, Wilkins TA (1994) A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.). Anal Biochem 223:7–12
Weinl S, Kudla J (2009) The CBL–CIPK Ca2+-decoding signaling network: function and perspectives. New Phytol 184:517–528. https://doi.org/10.1111/j.1469-8137.2009.02938.x
Xu W, Dubos C, Lepiniec L (2015) Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci 20:176–185. https://doi.org/10.1016/j.tplants.2014.12.001
Yamada M, Sato A (2002) Segregation for fruit astringency type in progenies derived from crosses of ‘Nishimurawase’ × pollination constant non-astringent genotypes in oriental persimmon (Diospyros kaki Thunb.). Sci Hortic 92:107–111. https://doi.org/10.1016/S0304-4238(01)00285-0
Yonemori K, Matsushima J (1985) Property of development of tannin cells in non-astringent type fruits of Japanese persimmon (Diospyros kaki) and its relationship to natural deastringency. J Jpn Soc Hortic Sci 54:201–208
Yonemori K, Sugiura A, Yamada M (2000) Persimmon genetics and breeding. Plant Breed Rev 19:191–225
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14. https://doi.org/10.1186/gb-2010-11-2-r14
Zoratti L, Karppinen K, Luengo Escobar A, Häggman H, Jaakola L (2014) Light-controlled flavonoid biosynthesis in fruits. Front Plant Sci 5:534. https://doi.org/10.3389/fpls.2014.00534
Acknowledgements
We thank Dr. Takashi Akagi (Kyoto University) for critical advice and discussions on data interpretation. We also appreciate bioinformatics support from Dr. Luca Comai and Dr. Isabelle M Henry (UC Davis).
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This work was supported by Grant-in-Aid for JSPS Research Fellow to SN (Grant number JP16J10408), and for Scientific Research (B) to KY (Grant number JP16H04876) from Japan Society for the Promotion of Science.
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The authors declare that they have no conflicts of interest.
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Nishiyama, S., Onoue, N., Kono, A. et al. Characterization of a gene regulatory network underlying astringency loss in persimmon fruit. Planta 247, 733–743 (2018). https://doi.org/10.1007/s00425-017-2819-0
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DOI: https://doi.org/10.1007/s00425-017-2819-0