Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Reddy, Umesh K ^a   Almeida, Aldo ^a   Abburi, Venkata L ^a   Alaparthi, Suresh Babu ^a   Unselt, Desiree ^a   Hankins, Gerald ^a   Park, Minkyu ^b   Choi, Doil ^b   Nimmakayala, Padma ^a  

^a WEST VIRGINIA STATE UNIVERSITY   (United States)

^b Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSAICIN; CAPSAICINOID; PARA COUMARIC ACID; UNCLASSIFIED DRUG;

ARTICLE; BIOACCUMULATION; BIOSYNTHESIS; CAPSICUM ANNUUM; CCR GENE; GENE; GENE EXPRESSION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HCT GENE; KAS GENE; METABOLITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRECURSOR; PROMOTER REGION; PUN1 GENE; SEASONAL VARIATION; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; CAPSAICIN; CAPSICUM; CHROMOSOME MAPPING; DNA PRIMERS; GENES, PLANT; GENETIC ASSOCIATION STUDIES; METABOLIC NETWORKS AND PATHWAYS; METABOLOME; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 84899991258     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086393     Document Type: Article

References (48)

1. FAOStat (2011) Available: http://faostat.fao.org/site/567/DestopDefault. aspx?PageID=567#ancor.FAO.
2. Wahyuni Y, Ballester A-R, Sudarmonowati E, Bino RJ, Bovy AG (2011) Metabolite biodiversity in pepper (Capsicum) fruits of thirty-two diverse accessions: Variation in health-related compounds and implications for breeding. Phytochemistry 72: 1358-1370.
3. Fujiwake H, Suzuki T, Iwai K (1982) Capsaicinoid Formation in the Protoplast from the Placenta of Capsicum Fruits. Agricultural and Biological Chemistry 46: 2591-2592.
4. Minguez-Mosquera MI, Hornero-Mendez D (1993) Separation and quantification of the carotenoid pigments in red peppers (Capsicum annuum L.), paprika, and oleoresin by reversed-phase HPLC. Journal of Agricultural and Food Chemistry 41: 1616-1620.
5. Lee RJ, Yolton RL, Yolton DP, Schnider C, Janin ML (1996) Personal defense sprays : effects and management of exposure. Journal of the American Optometric Association 67: 548-560.
6. McCormack P (2010) Capsaicin Dermal Patch. Drugs 70: 1831-1842.
7. Caterina MJ, Schumacher MA, Tominaga M, Rosen TA, Levine JD, et al. (1997) The capsaicin receptor: a heat-activated ion channel in the pain pathway. Nature 389: 816-824. (Pubitemid 27462969)
8. Marzo VD (2004) Signalling at vanilloid TRPV1 channels. European Journal of Biochemistry 271: 1813-1813.
9. Mazourek M, Pujar A, Borovsky Y, Paran I, Mueller L, et al. (2009) A dynamic interface for capsaicinoid symstems biology. Plant Physiology 150: 1806-1821.
10. Leete E, Louden MCL (1968) Biosynthesis of capsaicin and dihydrocapsaicin in Capsicum frutescens. Journal of the American Chemical Society 90: 6837-6841.
11. Kopp B, Jurenitsch J (1981) Biosynthese der Capsaicinoide in Capsicum annuum L. var. annuum. Planta Med 43: 272-279.
12. Aluru MR, Mazourek M, Landry LG, Curry J, Jahn M, et al. (2003) Differential expression of fatty acid synthase genes, Acl, Fat and Kas, in Capsicum fruit. Journal of Experimental Botany 54: 1655-1664. (Pubitemid 36821527)
13. Abraham-Juárez MR, Rocha-Granados MC, López MG, Rivera-Bustamante RF, Ochoa-Alejo N (2008) Virus-induced silencing of Comt, pAmt and Kas genes results in a reduction of capsaicinoid accumulation in chili pepper fruits. Planta 227: 681-695.
14. Dixon RA, Paiva NL (1995) Stress-induced phenylpropanoid metabolism. The Plant Cell 7: 1085-1097.
15. Lacombe E, Hawkins S, Van Doorsselaere J, Piquemal J, Goffner D, et al. (1997) Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. The Plant Journal 11: 429-441. (Pubitemid 27158950)
16. Lefebvre V, Palloix A, Caranta C, Pochard E (1995) Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 38: 112-121.
17. Blum E, Liu K, Mazourek M, Yoo EY, Jahn M, et al. (2002) Molecular mapping of the C locus for presence of pungency in Capsicum. Genome 45: 702-705. (Pubitemid 35368855)
18. Blum E, Mazourek M, O'Connell M, Curry J, Thorup T, et al. (2003) Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci analysis for capsaicinoid content in Capsicum. Theoretical and Applied Genetics 108: 79-86. (Pubitemid 38097984)
19. Kim M, Kim S, Kim S, Kim B-D (2001) Isolation of cDNA clones differentially accumulated in the placenta of pungent pepper by suppression subtractive hybridization. Molecules and Cells 11: 213-219. (Pubitemid 33663360)
20. Stewart C, Kang B-C, Liu K, Mazourek M, Moore SL, et al. (2005) The Pun1 gene for pungency in pepper encodes a putative acyltransferase. The Plant Journal 42: 675-688. (Pubitemid 40809886)
21. Stewart C, Mazourek M, Stellari GM, O'Connell MA, Jahn M (2007) Genetic control of pungency in C. chinense via the Pun1 locus. Journal of Experimental Botany 58: 979-991. (Pubitemid 46623307)
22. Stellari GM, Mazourek M, Jahn MM (2010) Contrasting modes for loss of pungency between cultivated and wild species of Capsicum. Heredity 104: 460-471.
23. Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, et al. (2013) Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE 8: e56200.
24. Han K, Jeong H-J, Sung J, Keum Y, Cho M-C, et al. (2013) Biosynthesis of capsinoid is controlled by the Pun1 locus in pepper. Molecular Breeding 31: 537-548.
25. Yumnam J, Tyagi W, Pandey A, Meetei NT, Rai M (2012) Evaluation of Genetic Diversity of Chilli Landraces from North Eastern India Based on Morphology, SSR Markers and the Pun1 Locus. Plant Molecular Biology Reporter 30: 1470-1479.
26. Bennett DJ, Kirby GW (1968) Constitution and biosynthesis of capsaicin. Journal of the Chemical Society C: Organic: 442-446.
27. Collins MD, Wasmund LM, Bosland PW (1995) Improved method for quantifying capsaicinoids in Capsicum using high-performance liquid chromatography. HortScience 30: 137-139.
28. Zewdie Y, Bosland PW (2001) Capsaicinoid profiles are not good chemotaxonomic indicators for Capsicum species. Biochemical Systematics and Ecology 29: 161-169. (Pubitemid 32056106)
29. Iwai K, Suzuki T, Fujiwake H (1979) Formation and accumulation of pungent principle of hot pepper fruits, capsaicin and its analogues, in Capsicum annuun var. annuun cv. Karayatsubusa at different growth stages after flowering. Agricultural and Biological Chemistry 43: 2493-2498.
30. Rozen S, Skaletsky HJ (1998) Primer3. Available: http:// biotoolsumassmededu/bioapps/primer3-wwwcgi.
31. Wheelan SJ, Church DM, Ostell JM (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Research 11: 1952-1957. (Pubitemid 33100436)
32. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
33. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
34. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Research 27: 297-300. (Pubitemid 29209466)
35. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The Structure of Haplotype Blocks in the Human Genome. Science 296: 2225-2229. (Pubitemid 34680308)
36. Fallin D, Schork NJ (2000) Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data. The American Journal of Human Genetics 67: 947-959.
37. Abburi L (2013) Linkage disequilibrium and population structure analysis among Capsicum annuum L. cultivars for use in association mapping. WV, USA: West Virginia State University.
38. Holm S (1979) A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6: 65-70.
39. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of royal statistical society 57: 289-300.
40. Winkel-Shirley B (2001) Flavonoid Biosynthesis. A Colorful Model for Genetics, Biochemistry, Cell Biology, and Biotechnology. Plant Physiology 126: 485-493.
41. Handrick V, Vogt T, Frolov A (2010) Profiling of hydroxycinnamic acid amides in Arabidopsis thaliana pollen by tandem mass spectrometry. Analytical and Bioanalytical Chemistry 398: 2789-2801.
42. Rao SR, Ravishankar GA (2000) Biotransformation of protocatechuic aldehyde and caffeic acid to vanillin and capsaicin in freely suspended and immobilized cell cultures of Capsicum frutescens. Journal of Biotechnology 76: 137-146.
43. Kawasaki T, Koita H, Nakatsubo T, Hasegawa K, Wakabayashi K, et al. (2006) Cinnamoyl-CoA reductase, a key enzyme in lignin biosynthesis, is an effector of small GTPase Rac in defense signaling in rice. Proceedings of the National Academy of Sciences of the United States of America 103: 230-235. (Pubitemid 43076132)
44. Wu FN, Mueller LA, Crouzillas D, Petiard V, Tanksley SD (2006) 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 174: 1407-1420. (Pubitemid 44808310)
45. Pichon M, Courbou I, Beckert M, Boudet A-M, Grima-Pettenati J (1998) Cloning and characterization of two maize cDNAs encoding Cinnamoyl-CoA Reductase (CCR) and differential expression of the corresponding genes. Plant Molecular Biology 38: 671-676. (Pubitemid 28456119)
46. Funk C, Brodelius PE (1990) Phenylpropanoid Metabolism in Suspension Cultures of Vanilla planifolia Andr. II. Effects of Precursor Feeding and Metabolic Inhibitors. Plant Physiology 94: 95-101. (Pubitemid 120030022)
47. Dehesh K, Tai H, Edwards P, Byrne J, Jaworski JG (2001) Overexpression of 3-Ketoacyl-Acyl-Carrier Protein Synthase IIIs in Plants Reduces the Rate of Lipid Synthesis. Plant Physiology 125: 1103-1114. (Pubitemid 32169915)
48. Leonard JM, Knapp SJ, Slabaugh MB (1998) A Cupheaß-ketoacyl-ACP synthase shifts the synthesis of fatty acids towards shorter chains in Arabidopsis seeds expressing Cuphea FatB thioesterases. The Plant Journal 13: 621-628. (Pubitemid 28178488)