Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties

BMC Genomics

Ralf G. Dietzgen¹  Michael J. Gidley¹  Gregory R. Monteith²  P. Nicholas Shaw¹  David J. Innes³  Van L. T. Hoang¹ 

[1] Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia;School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia;Department of Agriculture and Fisheries, Agri-Science Queensland, Brisbane, Queensland, Australia

关键词: Gene expression;    Nucleotide diversity;    Phenylpropanoid-flavonoid pathway;    Expressed sequence tags;    Mango fruit;   

Others  :  1221834
DOI  :  10.1186/s12864-015-1784-x

 received in 2015-02-08, accepted in 2015-07-17,  发布年份 2015

【 摘 要 】

Background

Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles.

Results

A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316 bp. Variety IW had the highest SNP frequency (one SNP every 258 bp) while KP and NDM had similar frequencies (one SNP every 369 bp and 360 bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3’-hydroxylase (F3’H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties.

Conclusions

The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango.

【 授权许可】

   
2015 Hoang et al.

【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

【 参考文献 】

• [1]Middleton E, Kandaswami C, Theoharides TC. The effects of plant flavonoids on mammalian cells: implications for inflammation, heart disease, and cancer. Pharmacol Rev. 2000; 52(4):673-751.
• [2]Burbulis IE, Winkel-Shirley B. Interactions among enzymes of the Arabidopsis flavonoid biosynthetic pathway. Proc Natl Acad Sci U S A. 1999; 96(22):12929-34.
• [3]de Vries GE. Flavonoid biosynthetic pathway. Trends Plant Sci. 2000; 5(1):7.
• [4]Cohen SD, Tarara JM, Gambetta GA, Matthews MA, Kennedy JA. Impact of diurnal temperature variation on grape berry development, proanthocyanidin accumulation, and the expression of flavonoid pathway genes. J Exp Bot. 2012; 63(7):2655-65.
• [5]Groenenboom M, Gomez-Roldan V, Stigter H, Astola L, van Daelen R, Beekwilder J, Bovy A, Hall R, Molenaar J. The flavonoid pathway in tomato seedlings: transcript abundance and the modeling of metabolite dynamics. PLoS ONE. 2013; 8(7):e68960.
• [6]Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR. The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity. Plant Physiol Biochem. 2013; 72:21-34.
• [7]Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NGM, Martinelli F, Sebastiani L, Tonutti P. Computational annotation of genes differentially expressed along olive fruit development. BMC Plant Biol. 2009; 9:128-45. BioMed Central Full Text
• [8]Martinelli F, Tonutti P. Flavonoid metabolism and gene expression in developing olive (Olea europaea L.) fruit. Pl Biosyst. 2012; 146:164-70.
• [9]Bally ISE, Lu P, Johnson PR. Mango breeding. In: Breeding Plantation Tree Crops: Tropical Species. Jain SM, Priyadarshan PM, editors. Springer, New York, USA; 2009: p.51-82.
• [10]Bally ISE. Advances in Research and Development of Mango Industry. Rev Bras Frutic. 2011; 33:57-63.
• [11]Masibo M, He Q. Mango bioactive compounds and related nutraceutical properties. Food Rev Int. 2009; 25:346-70.
• [12]Taing MW, Pierson JT, Hoang VL, Shaw PN, Dietzgen RG, Gidley MJ, Roberts-Thomson SJ, Monteith GR. Mango fruit peel and flesh extracts affect adipogenesis in 3T3-L1 cells. Food Funct. 2012; 3:828-36.
• [13]Pierson JT, Monteith GR, Roberts-Thomson SJ, Dietzgen RG, Gidley MJ, Shaw PN. Phytochemical extraction, characterisation and comparative distribution across four mango (Mangifera indica L.) fruit varieties. Food Chem. 2014; 149:253-63.
• [14]Hossain MA, Rana MM, Kimura Y, Roslan HA. Changes in biochemical characteristics and activities of ripening associated enzymes in mango fruit during the storage at different temperatures. BioMed Res Int. 2014; 2014:232969.
• [15]Palafox-Carlos H, Contreras-Vergara CA, Muhlia-Almazan A, Islas-Osuna MA, Gonzalez-Aguilar GA. Expression and enzymatic activity of phenylalanine ammonia-lyase and p-coumarate 3-hydroxylase in mango (Mangifera indica ‘Ataulfo’) during ripening. Genet Mol Res. 2014; 13(2):3850-8.
• [16]Ish-Shalom M, Dahan Y, Maayan I, Irihimovitch V. Cloning and molecular characterization of an ethylene receptor gene, MiERS1, expressed during mango fruitlet abscission and fruit ripening. Plant Physiol Biochem. 2011; 49(8):931-6.
• [17]Chidley HG, Kulkarni RS, Pujari KH, Giri AP, Gupta VS. Spatial and temporal changes in the volatile profile of Alphonso mango upon exogenous ethylene treatment. Food Chem. 2013; 136(2):585-94.
• [18]Joulain D. J Agric Food Chem. 2005; 53(21):8418.
• [19]Ornelas-Paz JD, Yahia EM, Gardea AA. Changes in external and internal color during postharvest ripening of ‘Manila’ and ‘Ataulfo’ mango fruit and relationship with carotenoid content determined by liquid chromatography-APcI(+)-time-of-flight mass spectrometry. Postharvest Biol Technol. 2008; 50:145-52.
• [20]Pandit SS, Kulkarni RS, Giri AP, Kollner TG, Degenhardt J, Gershenzon J, Gupta VS. Expression profiling of various genes during the fruit development and ripening of mango. Plant Physiol Biochem. 2010; 48(6):426-33.
• [21]Wu HX, Jia HM, Ma XW, Wang SB, Yao QS, Xu WT, Zhou YG, Gao ZS, Zhan RL. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits. J Proteomics. 2014; 105:19-30.
• [22]Azim MK, Khan IA, Zhang Y. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. Plant Mol Biol. 2014; 85(1–2):193-208.
• [23]Luria N, Sela N, Yaari M, Feygenberg O, Kobiler I, Lers A, Prusky D. De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment. BMC Genomics. 2014; 15:957. BioMed Central Full Text
• [24]Clotault J, Peltier D, Soufflet-Freslon V, Briard M, Geoffriau E. Differential selection on carotenoid biosynthesis genes as a function of gene position in the metabolic pathway: a study on the carrot and dicots. PLoS ONE. 2012; 7(6): Article ID e38724
• [25]Guerra R, Yu Z. Single Nucleotide Polymorphisms and Their Applications. In: Computational and Statistical Approaches to Genomics. Zhang W, Shmulevich I, editors. Springer, US; 2006: p.311-49.
• [26]Brookes AJ. The essence of SNPs. Gene. 1999; 234(2):177-86.
• [27]Ganal MW, Altmann T, Roder MS. SNP identification in crop plants. Curr Opin Plant Biol. 2009; 12(2):211-7.
• [28]Aguade M. Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol Biol Evol. 2001; 18(1):1-9.
• [29]Andersen JR, Zein I, Wenzel G, Darnhofer B, Eder J, Ouzunova M, Lübberstedt T. Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds. BMC Plant Biol. 2008; 8:2-16. BioMed Central Full Text
• [30]Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A. Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics. 2003; 270(1):24-33.
• [31]Dillon NL, Bally ISE, Wright CL, Hucks L, Innes DJ, Dietzgen RG. Genetic diversity of the Australian National Mango Genebank. Sci Hort. 2013; 150:213-26.
• [32]Rajendran P, Ekambaram G, Sakthisekaran D. Effect of mangiferin on benzo(a)pyrene induced lung carcinogenesis in experimental Swiss albino mice. Nat Prod Res. 2008; 22:672-80.
• [33]Hoang VLT, Pierson J-T, Curry MC, Shaw PN, Dietzgen RG, Gidley MJ, et al. Polyphenolic contents and the effects on breast cancer cells of methanolic extracts from various mango varieties. Food Sci Biotechnol. 2014, Accepted.
• [34]Lou C, He X-H, H C, Hu Y, Ou S-J. Molecular cloning and expression analysis of four actin genes (MiACT) from mango. Bio Plantarum. 2013. 57:238–44.
• [35]Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L et al.. Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol. 2006; 15:1367-78.
• [36]Van K, Hwang EY, Kim MY, Kim YH, Cho YI, Cregan PB, Lee SH. Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica. 2004; 139:147-57.
• [37]Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45.
• [38]Chagne D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A et al.. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE. 2012; 7(2): Article ID e31745
• [39]Lu Y, Rausher MD. Evolutionary rate variation in anthocyanin pathway genes. Mol Biol Evol. 2003; 20(11):1844-53.
• [40]Livingstone K, Anderson S. Patterns of variation in the evolution of carotenoid biosynthetic pathway enzymes of higher plants. J Hered. 2009; 100(6):754-61.
• [41]Chagne D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EH, Gardiner SE, Korban SS. Development of a set of SNP markers present in expressed genes of the apple. Genomics. 2008; 92(5):353-8.
• [42]Adato A, Mandel T, Mintz-Oron S, Venger I, Levy D, Yativ M, Domínguez E, Wang Z, De Vos RCH, Jetter R et al.. Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network. PLoS Genet. 2009; 5:1-23.
• [43]Verhoeyen ME, Bovy A, Collins G, Muir S, Robinson S, de Vos CH, Colliver S. Increasing antioxidant levels in tomatoes through modification of the flavonoid biosynthetic pathway. J Exp Bot. 2002; 53(377):2099-106.
• [44]Cheng GW, Breen PJ. Activity of phenylalanine ammonia-lyase (PAL) and concentrations of anthocyanins and phenolics in developing strawberry fruit. J Am Soc Hortic Sci. 1991; 116:865-9.
• [45]Singh R, Rastogi S, Dwivedi UN. Phenylpropanoid Metabolism in Ripening Fruits. Compr Rev Food Sci Food Saf. 2010; 9:398-416.
• [46]Salvatierra A, Pimentel P, Moya-Leon MA, Caligari PDS, Herrera R. Comparison of transcriptional profiles of flavonoid genes and anthocyanin contents during fruit development of two botanical forms of Fragaria chiloensis ssp. chiloensis. Phytochemistry. 2010; 71:1839-47.
• [47]Boss PK, Davies C, Robinson SP. Analysis of the Expression of Anthocyanin Pathway Genes in Developing Vitis vinifera L. cv Shiraz Grape Berries and the Implications for Pathway Regulation. Plant Physiol. 1996; 111(4):1059-66.
• [48]Liu Y, Shi Z, Maximova S, Payne MJ, Guiltinan MJ. Proanthocyanidin synthesis in Theobroma cacao: genes encoding anthocyanidin synthase, anthocyanidin reductase, and leucoanthocyanidin reductase. BMC Plant Biol. 2013; 13:202. BioMed Central Full Text
• [49]Ashihara H, Deng WW, Mullen W, Crozier A. Distribution and biosynthesis of flavan-3-ols in Camellia sinensis seedlings and expression of genes encoding biosynthetic enzymes. Phytochemistry. 2010; 71(5–6):559-66.
• [50]Xiaonan Z, Qing C, Dingqun Y, Shuli Z, Haoru T. Expression Analysis of the ANR and LAR Gene in Fragaria × ananassa cv. Toyonaka J Agr Sci. 2013; 5(2):64-9.
• [51]Pfeiffer J, Kuhnel C, Brandt J, Duy D, Punyasiri PA, Forkmann G, Fischer TC. Biosynthesis of flavan 3-ols by leucoanthocyanidin 4-reductases and anthocyanidin reductases in leaves of grape (Vitis vinifera L.), apple (Malus x domestica Borkh.) and other crops. Plant Physiol Biochem. 2006; 44(5–6):323-34.
• [52]Bogs J, Downey MO, Harvey JS, Ashton AR, Tanner GJ, Robinson SP. Proanthocyanidin synthesis and expression of genes encoding leucoanthocyanidin reductase and anthocyanidin reductase in developing grape berries and grapevine leaves. Plant Physiol. 2005; 139(2):652-63.
• [53]Devic M, Guilleminot J, Debeaujon I, Bechtold N, Bensaude E, Koornneef M, Pelletier G, Delseny M. The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development. Plant J. 1999; 19(4):387-98.
• [54]Fujita A, Goto-Yamamoto N, Aramaki I, Hashizume K. Organ-specific transcription of putative flavonol synthase genes of grapevine and effects of plant hormones and shading on flavonol biosynthesis in grape berry skins. Biosci Biotechnol Biochem. 2006; 70(3):632-8.
• [55]Malik AU, Singh Z. Pre-storage application of polyamines improves shelf-life and fruit quality in mango. J Hortic Sci Biotech. 2005; 80:363-9.
• [56]Chang S, Puryear J, Cairney J. A simple and effcient method for isolating RNA from pine trees. Plan Mol Biol Rep. 1993; 11:113-6.
• [57]Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28(12): 1647-1649.
• [58]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-10.
• [59]Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000; 132:365-86.
• [60]Singh RK, Ali SA, Nath P, Sane VA. Activation of ethylene-responsive p-hydroxyphenylpyruvate dioxygenase leads to increased tocopherol levels during ripening in mango. J Exp Bot. 2011; 62(10):3375-85.
• [61]Devitt LC, Fanning K, Dietzgen RG, Holton TA. Isolation and functional characterization of a lycopene b-cyclase gene that controls fruit colour of papaya (Carica papaya L.). J Exp Bot. 2010; 61:33-9.
• [62]Giuntini D, Lazzeri V, Calvenzani V, Dall’Asta C, Galaverna G, Tonelli C, Petroni K, Ranieri A. Flavonoid profiling and biosynthetic gene expression in flesh and peel of two tomato genotypes grown under UV-B-depleted conditions during ripening. J Agric Food Chem. 2008; 56(14):5905-15.
• [63]Pfaffl MW. Chapter3. Quantification strategies in real-time PCR. In: A-Z of quantitative PCR. Bustin SA, editor. International University Line, La Jolla, CA, USA; 2004: p.87-112.
• [64]Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004; 37(6):914-39.