Location of chlorogenic acid biosynthesis pathway and poliphenol oxidase genes in a new interspecific anchored linkage map of eggplant

Background Eggplant is a powerful source of polyphenols which seems to play a key role in the prevention of several human diseases, such as cancer and diabetes. Chlorogenic acid is the polyphenol most present in eggplant, comprising between the 70% and 90% of the total polyphenol content. Introduction of the high chlorogenic acid content of wild relatives, such as S. incanum, into eggplant varieties will be of great interest. A potential side effect of the increased level polyphenols could be a decrease on apparent quality due to browning caused by the polyphenol oxidase enzymes mediated oxidation of polyphenols. We report the development of a new interspecific S. melongena × S. incanum linkage map based on a first backcross generation (BC1) towards the cultivated S. melongena as a tool for introgressing S. incanum alleles involved in the biosynthesis of chlorogenic acid in the genetic background of S. melongena. Results The interspecific genetic linkage map of eggplant developed in this work anchor the most informative previously published genetic maps of eggplant using common markers. The 91 BC1 plants of the mapping population were genotyped with 42 COSII, 99 SSRs, 88 AFLPs, 9 CAPS, 4 SNPs and one morphological polymorphic markers. Segregation marker data resulted in a map encompassing 1085 cM distributed in 12 linkage groups. Based on the syntheny with tomato, the candidate genes involved in the core chlorogenic acid synthesis pathway in eggplant (PAL, C4H, 4CL, HCT, C3′H, HQT) as well as five polyphenol oxidase (PPO1, PPO2, PPO3, PPO4, PPO5) were mapped. Except for 4CL and HCT chlorogenic acid genes were not linked. On the contrary, all PPO genes clustered together. Candidate genes important in domestication such as fruit shape (OVATE, SISUN1) and prickliness were also located. Conclusions The achievements in location of candidate genes will allow the search of favorable alleles employing marker-assisted selection in order to develop new varieties with higher chlorogenic content alongside a lower polyphenol oxidase activity. This will result into an enhanced product showing a lower fruit flesh browning with improved human health properties.This research has been partially funded by Ministerio de Economa y Competitividad and FEDER (grant AGL2012-34213). Pietro Gramazio is grateful to Universitat Politcnica de Valncia for a pre-doctoral grant.Gramazio, P.; Prohens Tomás, J.; Plazas Ávila, MDLO.; Andújar Pérez, I.; Herraiz García, FJ.; Castillo Lorenzo, E.; Knapp, S.... (2014). Location of chlorogenic acid biosynthesis pathway and poliphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biology. 14(350):1-15. https://doi.org/10.1186/s12870-014-0350-z11514350Daunay MC, Lester RN: Eggplant. Tropical Plant Breeding. Edited by: Charrier A, Jacquot M, Hamon S, Nicolas D. 2001, CIRAD, SciencePublishers Inc, Plymouth, UK, 199-221.Hanson PM, Yang R, Tsou S, Ledesma D, Engle L, Lee T: Diversity in eggplant (Solanum melongena) for superoxide scavenging activity, total phenolics, and ascorbic acid. J Food Compos Anal. 2006, 19: 594-600. 10.1016/j.jfca.2006.03.001.Lo Scalzo R, Fibiani M, Mennella G, Rotino GL, Dal Sasso M, Culici M, Spallino A, Braga PC: Thermal treatment of eggplant (Solanum melongena L.) increases the antioxidant content and the inhibitory effect on human neutrophil burst. J Agric Food Chem. 2010, 58: 3371-3379. 10.1021/jf903881s.Plazas M, López-Gresa MP, Vilanova S, Torres C, Hurtado M, Gramazio P, Andújar I, Herráiz FJ, Bellés JM, Prohens J: Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning. J Agric Food Chem. 2013, 61: 8871-8879. 10.1021/jf402429k.Plazas M, Andújar I, Vilanova S, Hurtado M, Gramazio P, Herraiz FJ, Prohens J: Breeding for chlorogenic acid content in eggplant: interest and prospects. Not Bot Horti Agrobot Cluj-Napoca. 2013, 41 (1): 26-35.Mennella G, Lo Scalzo R, Fibiani M, D’Alessandro A, Francese G, Toppino L, Acciarri N, de Almeida AE, Rotino GL: Chemical and bioactive quality traits during fruit ripening in eggplant (S. melongena L.) and allied species. J Agric Food Chem. 2012, 60: 11821-11831. 10.1021/jf3037424.Prohens J, Whitaker BD, Plazas M, Vilanova S, Hurtado M, Blasco M, Gramazio P, Stommel JR: Genetic diversity in morphological characters and phenolic acids content resulting from an interspecific cross between eggplant, Solanum melongena, and its wild ancestor (S. incanum). Ann Appl Biol. 2013, 162: 242-257. 10.1111/aab.12017.Singh AP, Luthria D, Wilson T, Vorsa N, Singh V, Banuelos GS, Pasakdee S: Polyphenols content and antioxidant capacity of eggplant pulp. Food Chem. 2009, 114: 955-961. 10.1016/j.foodchem.2008.10.048.Stommel JR, Whitaker BD: Phenolic acid content and composition of eggplant fruit in a germplasm core subset. J Am Soc Hort Sci. 2003, 128: 704-710.Whitaker BD, Stommel JR: Distribution of hydroxycinnamic acid conjugates in fruit of commercial eggplant (Solanum melongena L.) cultivars. J Agric Food Chem. 2003, 51: 3448-3454. 10.1021/jf026250b.Cho A, Jeon S, Kim M, Yeo J, Seo K, Choi M, Lee M: Chlorogenic acid exhibits anti-obesity property and improves lipid metabolism in high-fat diet-induced-obese mice. Food Chem Toxicol. 2010, 48: 937-943. 10.1016/j.fct.2010.01.003.Dos Santos MD, Almeida MC, Lopes NP, De Souza GEP: Evaluation of the anti-inflammatory, analgesic and antipyretic activities of the natural polyphenol chlorogenic acid. Biol Pharm Bull. 2006, 29: 2236-2240. 10.1248/bpb.29.2236.Luthria D, Singh AP, Wilson T, Vorsa N, Banuelos GS, Vinyard BT: Influence of conventional and organic agricultural practices on the phenolic content in eggplant pulp: plant-to-plant variation. Food Chem. 2010, 121: 406-411. 10.1016/j.foodchem.2009.12.055.Lester RN, Hasan SMZ: Origin and domestication of the brinjal eggplant, Solanum melongena, from S. incanum, in Africa and Asia. Solanaceae III: Taxonomy, Chemistry, Evolution. Edited by: Hawkes JG, Lester RN, Nee MH, Estrada N. 1991, Royal Botanic Gardens, Kew, London, UK, 369-388.Knapp S, Vorontsova MS, Prohens J: Wild relatives of the eggplant (Solanum melongena L.: Solanaceae): new understanding of species names in a complex group. PLoS One 2013, 8:e57039.,Ma C, Dastmalchi K, Whitaker BD, Kennelly EJ: Two new antioxidant malonated caffeoylquinic acid isomers in fruits of wild eggplant relatives. J Agric Food Chem. 2011, 59: 9645-9651. 10.1021/jf202028y.Ramirez EC, Whitaker JR, Virador VM: Polyphenol Oxidase. Handbook of Food Enzymology. Edited by: Whitaker JR, Voragen AGJ, Wong DWS. 2003, Marcel Dekker, Inc, New York, 509-524.Concellón A, Zaro MJ, Chaves AR, Vicente AR: Changes in quality and phenolic antioxidants in dark purple American eggplant (Solanum melongena L. cv. Lucía) as affected by storage at 0°C and 10°C. Postharvest Biol Technol. 2012, 66: 35-41. 10.1016/j.postharvbio.2011.12.003.Doğan M, Arslan O, Doğan S: Substrate specificity, heat inactivation and inhibition of polyphenol oxidase from different aubergine cultivars. Int J Food Sci Tech. 2002, 37: 415-423. 10.1046/j.1365-2621.2002.00580.x.Shetty SM, Chandrashekar A, Venkatesh YP: Eggplant polyphenol oxidase multigene family: cloning, phylogeny, expression analyses and immunolocalization in response to wounding. Phytochemistry. 2011, 72: 2275-2287. 10.1016/j.phytochem.2011.08.028.Comino C, Lanteri S, Portis E, Acquadro A, Romani A, Hehn A, Larbat R, Bourgaud F: Isolation and functional characterization of a cDNA coding a hydroxycinnamoyltransferase involved in phenylpropanoid biosynthesis in Cynara cardunculus L. BMC Plant Biol 2007, 7:14.,Comino C, Hehn A, Moglia A, Menin B, Bourgaud F, Lanteri S, Portis E: The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway. BMC Plant Biol 2009, 9:30.,Menin B, Comino C, Moglia A, Dolzhenko Y, Portis E, Lanteri S: Identification and mapping of genes related to caffeoylquinic acid synthesis in Cynara cardunculus L. Plant Sci. 2010, 179: 338-347. 10.1016/j.plantsci.2010.06.010.Niggeweg R, Michael A, Martin C: Engineering plants with increased levels of the antioxidant chlorogenic acid. Nat Biotechnol. 2004, 22: 746-754. 10.1038/nbt966.Nunome T, Ishiguro K, Yoshida T, Hirai M: Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers. Breed Sci. 2001, 51: 19-26. 10.1270/jsbbs.51.19.Nunome T, Suwabe K, Ohyama A, Fukuoka H: Characterization of trinucleotide microsatellites in eggplant. Breed Sci. 2003, 53: 77-83. 10.1270/jsbbs.53.77.Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H: Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet. 2009, 119: 1143-1153. 10.1007/s00122-009-1116-0.Doganlar S, Frary A, Daunay M, Lester RN, Tanksley SD: A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae. Genetics. 2002, 161: 1697-1711.Wu F, Eannetta NT, Xu Y, Tanksley SD: A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet. 2009, 118: 927-935. 10.1007/s00122-008-0950-9.Doganlar S, Frary A, Daunay M, Huvenaars K, Mank R, Frary A: High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae. Euphytica. 2014, 197: 211-228. 10.1007/s10681-013-1060-6.Barchi L, Lanteri S, Portis E, Stàgel A, Valè G, Toppino L, Rotino GL: Segregation distortion and linkage analysis in eggplant (Solanum melongena L.). Genome. 2010, 53: 805-815. 10.1139/G10-073.Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A: Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet. 2012, 125: 47-56. 10.1007/s00122-012-1815-9.Barchi L, Lanteri S, Portis E, Valè G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L: A RAD Tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS One 2012, 7:e43740.,Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD: Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell. 2002, 14: 1457-1467. 10.1105/tpc.010479.The Angiosperm Phylogeny Group: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc. 2003, 141: 399-436. 10.1046/j.1095-8339.2003.t01-1-00158.x.Vilanova S, Manzur JP, Prohens J: Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Mol Breed. 2012, 30: 647-660. 10.1007/s11032-011-9650-2.Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A: Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato. Gene. 2010, 450: 76-84. 10.1016/j.gene.2009.10.006.Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL: Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 2011, 12:304.,Jeuken M, Van Wijk R, Peleman J, Lindhout P: An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. sativa × L. saligna F2 populations. Theor Appl Genet. 2001, 103: 638-647. 10.1007/s001220100657.Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S: Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence. Mol Breed. 2013, 31: 101-110. 10.1007/s11032-012-9774-z.Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA, Miedaner T, Würschum T: Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genomics 2011, 12:380.,Ren Y, McGregor C, Zhang Y, Gong G, Zhang H, Guo S, Sun H, Cai W, Zhang J, Xu Y: An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus). BMC Plant Biol 2014, 14:33.,Prohens J, Rodríguez-Burruezo A, Raigón MD, Nuez F: Total phenolic concentration and browning susceptibility in a collection of different varietal types and hybrids of eggplant: implications for breeding for higher nutritional quality and reduced browning. J Am Soc Hort Sci. 2007, 132: 638-646.Raigón MD, Prohens J, Muñoz-Falcón JE, Nuez F: Comparison of eggplant landraces and commercial varieties for fruit content of phenolics, minerals, dry matter and protein. J Food Compos Anal. 2008, 21: 370-376. 10.1016/j.jfca.2008.03.006.Byrne P, McMullen M: Defining genes for agricultural traits: QTL analysis and the candidate gene approach. Proc Natl Acad Sci U S A. 1996, 7: 24-27.Vogt T: Phenylpropanoid biosynthesis. Mol Plant. 2010, 3: 2-20. 10.1093/mp/ssp106.Shi R, Shuford CM, Wang JP, Sun Y, Yang Z, Chen H, Tunlaya-Anukit S, Li Q, Liu J, Muddiman DC: Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa . Planta. 2013, 238: 487-497. 10.1007/s00425-013-1905-1.Kumar A, Ellis BE: The phenylalanine ammonia-lyase gene family in raspberry. structure, expression, and evolution. Plant Physiol. 2001, 127: 230-239. 10.1104/pp.127.1.230.Chagné D, Krieger C, Rassam M, Sullivan M, Fraser J, André C, Pindo M, Troggio M, Gardiner SE, Henry RA: QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biol 2012, 12:12.,Moglia A, Comino C, Menin B, Portis E, Aquadro A, Beekwilder MJ, Hehn A, Bourgaud F, Lanteri S: Caffeoylquinic acids biosynthesis and accumulation in Cynara cardunculus: state of the art. Acta Hort. 2013, 983: 401-405.Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S: Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor Appl Genet. 2009, 120: 59-70. 10.1007/s00122-009-1159-2.Portis E, Scaglione D, Acquadro A, Mauromicale G, Mauro R, Knapp SJ, Lanteri S: Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex. BMC Res Notes 2012, 5:252.,Rommens CM, Richael CM, Yan H, Navarre DA, Ye J, Krucker M, Swords K: Engineered native pathways for high kaempferol and caffeoylquinate production in potato. Plant Biotechnol J. 2008, 6: 870-886. 10.1111/j.1467-7652.2008.00362.x.André CM, Schafleitner R, Legay S, Lefèvre I, Aliaga CAA, Nomberto G, Hoffmann L, Hausman J, Larondelle Y, Evers D: Gene expression changes related to the production of phenolic compounds in potato tubers grown under drought stress. Phytochemistry. 2009, 70: 1107-1116. 10.1016/j.phytochem.2009.07.008.Di Guardo M, Tadiello A, Farneti B, Lorenz G, Masuero D, Vrhovsek U, Costa G, Velasco R, Costa F: A multidisciplinary approach providing new insight into fruit flesh browning physiology in apple (Malus x domestica Borkh.). PLoS One 2013, 8:e78004.,Urbany C, Stich B, Schmidt L, Simon L, Berding H, Junghans H, Niehoff KH, Braun A, Tacke E, Hofferbert HR, Lubeck J, Strahwald J, Gebhardt C: Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration. BMC Genomics 2011, 12:7.,Coetzer C, Corsini D, Love S, Pavek J, Tumer N: Control of enzymatic browning in potato (Solanum tuberosum L.) by sense and antisense RNA from tomato polyphenol oxidase. J Agric Food Chem. 2001, 49: 652-657. 10.1021/jf001217f.Murata M, Nishimura M, Murai N, Haruta M, Homma S, Itoh Y: A transgenic apple callus showing reduced polyphenol oxidase activity and lower browning potential. Biosci Biotechnol Biochem. 2001, 65: 383-388. 10.1271/bbb.65.383.Chai C, Lin Y, Shen D, Wu Y, Li H, Dou D: Identification and functional characterization of the Soybean GmaPPO12 promoter conferring Phytophthora sojae induced expression. PLoS One 2013, 8:e67670.,Newman SM, Tantasawat P, Steffens JC: Tomato polyphenol oxidase B is spatially and temporally regulated during development and in response to ethylene. Molecules. 2011, 16: 493-517. 10.3390/molecules16010493.Tran L, Taylor J, Constabel C: The polyphenol oxidase gene family in land plants: lineage-specific duplication and expansion. BMC Genomics 2012, 13:395.,Yamakawa K, Mochizuki H: Nature and inheritance of Fusarium-wilt resistance in eggplant cultivars and related wild Solanum species. Bull Veg Orn Crops Res Stn. 1979, 6: 19-27.Stàgel A, Portis E, Toppino L, Rotino GL, Lanteri S: Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 2008, 9:357.,Frary A, Frary A, Daunay M, Huvenaars K, Mank R, Doğanlar S: QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis. Euphytica. 2014, 197: 211-228. 10.1007/s10681-013-1060-6.Portis E, Barchi L, Toppino L, Lanteri S, Acciarri N, Felicioni N, Fusari F, Barbierato V, Cericola F, Valè G, Rotino GL: QTL Mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS One 2014, 9:e89499.,Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H: Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 2014, 1–12. doi:10.1093/dnares/dsu027,Doyle J, Doyle J: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987, 19: 11-15.Wu F, Mueller LA, Crouzillat D, Pétiard V, Tanksley SD: Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006, 174: 1407-1420. 10.1534/genetics.106.062455.Kofler R, Schlötterer C, Lelley T: SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics. 2007, 23: 1683-1685. 10.1093/bioinformatics/btm157.Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA: The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 2011, 39: D1149-D1155. 10.1093/nar/gkq866.Vos P, Hogers R, Bleeker M, Reijans M, van De Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M: AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23: 4407-4414. 10.1093/nar/23.21.4407.Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999, 41: 95-98.Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Meth Protocols. 1999, 132: 365-386. 10.1385/1-59259-192-2:365.Huang Z, Van Houten J, Gonzalez G, Xiao H, van der Knaap E: Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol Genet Genomics. 2013, 288: 111-129. 10.1007/s00438-013-0733-0.Van Ooijen J: JoinMap 4. Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands. 2006Kosambi D: The estimation of map distances from recombination values. Ann Eugen. 1944, 12: 172-175. 10.1111/j.1469-1809.1943.tb02321.x.Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19: 1639-1645. 10.1101/gr.092759.109