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Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci analysis for capsaicinoid content in Capsicum

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Quantitative variation in the accumulation of two major capsaicinoids responsible for pungency in the fruit of chile peppers, capsaicin and dihydrocapsaicin, was analyzed in a cross between the non-pungent Capsicum annuum parent cv. Maor and a pungent Capsicum frutescens parent, accession BG 2816. In order to identify quantitative trait loci (QTLs) for capsaicinoid content, we employed the bulked segregant analysis method and screened bulked DNA from F2 individuals at the extremes of the distribution of capsaicinoid content with RAPD primers. Screening with 400 primers allowed the identification of three loci that were polymorphic between the bulks. These RAPD markers were converted to SCARs and subsequently mapped with additional RFLP markers to chromosome 7 of pepper. QTL interval analysis for individual and total capsaicinoid content identified a major QTL, termed cap, which explained 34–38% of the phenotypic variation for this trait in two growing environments. For all measurements, the allele of the pungent parent BG 2816 at cap contributed to the increased level of pungency. To determine whether known structural genes in the pathway could define a candidate for this QTL, 12 clones obtained from differentially expressed transcripts from placental tissue in pungent peppers were also mapped. None of them had a significant effect on this trait, nor did the allelic state at the locus C, the on/off switch for pungency in pepper, located on chromosome 2. The identity of cap and its effect on capsaicin content in other backgrounds will be addressed in future studies.

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  • Aluru MR, Mazourek M, Landry LG, Curry J, Jahn M, O'Connell MA (2003) Differential expression of fatty acid synthesis genes, Acl, Fat and Kas, in Capsicum fruit. J Exp Bot 54:1655–1664

    Article  CAS  PubMed  Google Scholar 

  • Ben Chaim A, Paran I, Grube R, Jahn M, van Wijk R, Peleman J (2001) QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor Appl Genet 102:1016–1028

    Article  Google Scholar 

  • Bennett DJ, Kirby GW (1968) Constitution and biosynthesis of capsaicin. J Chem Soc C:442–446

    Google Scholar 

  • Blum E, Liu K, Mazourek M, Yoo EY, Jahn M, Paran I (2002) Molecular mapping of the C locus for presence of pungency in Capsicum. Genome 45:702–705

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Wasmund LM, Bosland PW (1995) Improved method for quantifying capsaicinoids in Capsicum using high performance liquid chromatography. HortScience 30:137–139

    CAS  Google Scholar 

  • Cotter DJ (1980) A review of studies on chile. Agric Exp Sta Bull No 673, New Mexico State University, Las Cruces

  • Curry J, Aluru M, Mendoza M, Nevarez J, Melendrez M, O'Connell MA (1999) Transcripts for possible capsaicinoid biosynthetic genes are differentially accumulated in pungent and non-pungent Capsicum spp. Plant Sci 148:4757

    Article  CAS  Google Scholar 

  • Deshpande RB (1935) Studies in Indian chillies. 4. Inheritance of pungency in Capsicum annuum L. Indian J Agric Sci 5:513–516

    Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–14

    Google Scholar 

  • Franke R, Humphreys JM, Hemm MR, Denault JW, Ruegger MO, Cusumano JC, Chapple C (2002) The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism. Plant J 30:33–45

    Article  CAS  PubMed  Google Scholar 

  • Fujiwake H, Suzuki T, Oka S, Iwai K (1980) Enzymatic formation of capsaicinoid from vanillylamine and iso-type fatty acids by cell-free extracts of Capsicum annuum var. annuum cv. Karayatsubusa. Agric Biol Chem 44:2907–2912

    CAS  Google Scholar 

  • Gill KS, Ghai BS, Singh JR (1973) Inheritance of amount of capsaicin in chili (Capsicum frutescens L. and C. annuum L.). Indian J Agric Sci 43:839–841

    Google Scholar 

  • Greenleaf WH (1952) Inheritance of pungency and of the deciduous character in chili (Capsicum annuum). Proc Assoc 8th Agric Wkrs 49:110–111

    Google Scholar 

  • Harvell K, Bosland PW (1997) The environment produces a significant effect on pungency of chiles. HortScience 32:1292

    Google Scholar 

  • Hunziker AT (2001) The genera of Solanaceae, Gantner, Konigstein, pp 232–244

  • Kim M, Kim S, Kim S, Kim BD (2001) Isolation of cDNA clones differentially accumulated in the placenta of pungent pepper by suppression subtractive hybridization. Mol Cells 11:213–219

    CAS  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination frequency. Ann Eugen 12:172–175

    Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1993) Constructing a genetic linkage map with MAPMAKER/EXP v. 3.0: a tutorial and reference manual. Whitehead Institute Technical Report, Cambridge, Mass.

  • Livingstone KD, Lackney VK, Blauth J, Wijk VR, Jahn MK (1999) Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152:1183–1202

    CAS  PubMed  Google Scholar 

  • Leete E, Louden MCL (1968) Biosynthesis of capsaicin and dihydrocapsaicin in Capsicum frutescens. J Am Chem Soc 90:6837–6841

    CAS  PubMed  Google Scholar 

  • Mackay IJ, Caligari (2000) Efficiencies of F2 and backcross generation for bulked segregant analysis using dominant markers. Crop Sci 40:626–630

    Google Scholar 

  • Michelmore RW, Paran I, Kesseli R (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    PubMed  Google Scholar 

  • Nakayama RM, Matta FB (1985) "NuMex R Naky" chile pepper. HortScience 20:961–962

    Google Scholar 

  • Nelson CJ (1997) QGENE: software for marker-based genomic analysis and breeding. Mol Breed 3:229–235

    Article  Google Scholar 

  • Ooijen JW van, Boer MP, Jansen RC, Maliepaard C (2002) MapQTL 4.0, software for the calculation of QTL positions on genetic maps. Plant Research International, Wageningen, The Netherlands

  • Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993

    CAS  Google Scholar 

  • Rao GU, Paran I (2003) Polygalacturonase: a candidate gene for the soft flesh and deciduous fruit mutation in Capsicum. Plant Mol Biol 51:135–141

    CAS  PubMed  Google Scholar 

  • SAS Institute (1994) JMP users guide, version 3. SAS Institute, Cary, N.C.

  • Schoch G, Goepfert S, Morant M, Hehn A, Meyer D, Ullmann P, Werck-Reichhart D (2001) CYP98A3 from Arabidopsis thaliana is a 3-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway. J Biol Chem 276:36566–36574

    Article  CAS  PubMed  Google Scholar 

  • Wang GL, Paterson AH (1994) Assessment of DNA pooling strategies for mapping of QTLs. Theor Appl Genet 88:355–361

    Google Scholar 

  • Zewdie Y, Bosland PW (2000a) Capsaicinoid inheritance in an interspecific hybridization of Capsicum annuum × C. chinense. J Am Soc Hort Sci 125:448–453

    CAS  Google Scholar 

  • Zewdie Y, Bosland PW (2000b) Evaluation of genotype, environment, and genotype-by-environment interaction for capsaicinoids in Capsicum annuum L. Euphytica 111:185–190

    Article  CAS  Google Scholar 

  • Zewdie Y, Bosland PW (2001) Capsaicinoid profiles are not good chemotaxonomic indicators for Capsicum species. Biochem Syst Ecol 29:161–169

    Article  CAS  PubMed  Google Scholar 

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We thank Y. Borovsky for her help in RFLP analysis. This research was supported by the California Pepper Commission and the California Pepper Improvement Foundation, The United States-Israel Binational Agricultural Research and Development Fund Grant No. IS-3225-01C, USDA IFAF5 Award No. 2001-52100-113347, National Institutes of Health Award GM S06 GM08136, and a gift from Kalsec, Inc., Kalamazoo, Mich., USA.

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Correspondence to Ilan Paran.

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Communicated by J. Dvorak

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Blum, E., Mazourek, M., O'Connell, M. et al. Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci analysis for capsaicinoid content in Capsicum . Theor Appl Genet 108, 79–86 (2003).

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