Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL


Key message

Three novel QTL for peroxidase activity were mapped, and gene-specific markers for TaPod-A1 were developed and validated using RILs derived from the Doumai/Shi 4185 cross and 281 wheat cultivars. TaPod-A1 is within one of the three QTL.


Peroxidase (POD) activity in grain is an important factor determining the color of flour and end-use products of wheat, such as noodles and steamed bread. Mapping QTL for POD activity, characterization of POD genes and development of gene-specific markers are important for molecular marker-assisted selection in wheat breeding. Quantitative trait loci (QTL) for POD activity in common wheat were mapped using a recombinant inbred line (RIL) population derived from a Doumai/Shi 4185 cross grown in four environments and genotyped using the wheat 90 K iSelect assay. Three novel QTL for POD activity, QPod.caas-3AL, QPod.caas-4BS and QPod.caas-5AS, were identified on chromosomes 3AL, 4BS and 5AS, explaining 5.3–21.2 % of phenotypic variance across environments. The full-length genomic DNA (gDNA) sequence of a POD gene, designated TaPod-A1, on chromosome 3A was characterized by homolog cloning and PCR verification. Two complementary dominant sequence-tagged site (STS) markers, POD-3A1 and POD-3A2, were developed based on single nucleotide polymorphisms (SNPs) between two alleles at the TaPod-A1 locus, amplifying 291- and 766-bp fragments in cultivars with lower and higher POD activities, respectively. The two gene-specific markers were mapped on chromosome 3AL using a set of Chinese Spring (CS) nulli-tetrasomic lines, and ditelosomic lines 3AL and 3AS. QTL analysis indicated that QPod.caas-3AL co-segregated with the gene-specific markers POD-3A1 and POD-3A2. POD-3A1 and POD-3A2 were verified on 281 wheat cultivars and advanced lines, and showed significant (P < 0.05) associations with POD activities. POD-3A1 and POD-3A2 may be useful as markers for improving color attributes in wheat breeding programs.

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Fig. 1



Analysis of variance


Complementary DNA


Coding sequence


Chinese Spring


Genomic DNA


Logarithm of odds


Message RNA


Open reading frame


Polymerase chain reaction




Quantitative trait loci/locus


Recombinant inbred line


Single nucleotide polymorphism


Sequence-tagged site


Untranslated region




  1. Bérard A, Le Paslier MC, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C (2009) High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.). Plant Biotechnol J 7:364–374

    Article  PubMed  Google Scholar 

  2. Blee KA, Jupe SC, Richard G, Zimmerlin A, Davies DR, Paul Bolwell G (2001) Molecular identification and expression of the peroxidase responsible for the oxidative burst in French bean (Phaseolus vulgaris L.) and related members of the gene family. Plant Mol Biol 47:607–620

    CAS  Article  PubMed  Google Scholar 

  3. Boisson M, Mondon K, Torney V, Nicot N, Laine AL, Bahrman N, Gouy A, Daniel-Vedele F, Hirel B, Sourdille P, Dardevet M, Ravel C, Gouis L (2005) Partial sequences of nitrogen metabolism genes in hexaploid wheat. Theor Appl Genet 110:932–940

    CAS  Article  PubMed  Google Scholar 

  4. Borrelli GM, Troccoli A, Di Fonzo N, Fares C (1999) Durum wheat lipoxygenase activity and other quality parameters that affect pasta colour. Cereal Chem 76:335–340

    CAS  Article  Google Scholar 

  5. Borrelli GM, De Leonardis AM, Fares C, Platani C, Di Fonzo N (2003) Effect of modified processing conditions on oxidative properties of semolina dough and pasta. Cereal Chem 80:225–231

    CAS  Article  Google Scholar 

  6. Bosch A, Vega C, Benito C (1987) The peroxidase isozymes of the wheat kernel: tissue and substrate specificity and their chromosomal location. Theor Appl Genet 73:701–706

    CAS  Article  PubMed  Google Scholar 

  7. Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D’Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KFX, Edwards KJ, Bevan MW, Hall N (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  8. Feillet P, Autran JC, Icard-Vernière C (2000) Mini review pasta brownness: an assessment. J Cereal Sci 32:215–233

    CAS  Article  Google Scholar 

  9. Fraignier MP, Michaux-Ferrière N, Kobrehel K (2000) Distribution of peroxidase in durum wheat (Triticum durum). Cereal Chem 77:11–17

    CAS  Article  Google Scholar 

  10. Fry SC (1986) Cross-linking of matrix polymers in the growing cell walls of angiosperms. Annu Rev Plant Physiol 37:165–186

    CAS  Article  Google Scholar 

  11. Gélinas P, Poitras E, McKinnon CM, Morin A (1998) Oxido-reductases and lipases as dough-bleaching agents. Cereal Chem 75:810–814

    Article  Google Scholar 

  12. Geng HW, Xia XC, Zhang LP, Qu YY, He ZH (2012) Development of functional markers for a lipoxygenase gene TaLox-B1 on chromosome 4BS in common wheat. Crop Sci 52:568–576

    CAS  Article  Google Scholar 

  13. Giroux MJ, Morris CF (1997) A glycine to serine change in puroindoline b is associated with wheat grain hardness and low levels of starch-surface friabilin. Theor Appl Genet 95:857–864

    CAS  Article  Google Scholar 

  14. Goodin DB, McRee DE (1993) The Asp–His–iron triad of cytochrome c peroxidase controls the reduction potential electronic structure, and coupling of the tryptophan free radical to the heme. Biochemistry 32:3313–3324

    CAS  Article  PubMed  Google Scholar 

  15. Guillaumie S, Charmet G, Linossier L, Torney V, Robert N, Ravel C (2004) Colocation between a gene coding for the bZip factor SPA and an eQTL for a high-molecular-weight glutenin subunit in wheat (Triticum aestivum). Genome 47:705–713

    CAS  Article  PubMed  Google Scholar 

  16. Hemalatha MS, Manu BT, Bhagwat SG, Leelavathi K, Prasada Rao UJS (2007) Protein characteristics and peroxidase activities of different Indian wheat varieties and their relationship to chapatti-making quality. Eur Food Res Technol 225:463–471

    CAS  Article  Google Scholar 

  17. Hessler TG, Thomson MJ, Benscher D, Nachit MM, Sorrells ME (2002) Association of a lipoxygenase locus, Lpx-B1, with variation in lipoxygenase activity in durum wheat seeds. Crop Sci 42:1695–1700

    CAS  Article  Google Scholar 

  18. Hiraga S, Sasaki K, Ito H, Ohashi Y, Matsui H (2001) A large family of class III plant peroxidases. Plant Cell Physiol 42:462–468

    CAS  Article  PubMed  Google Scholar 

  19. Icard-Vernière C, Feillet P (1999) Effects of mixing conditions on pasta dough development and biochemical changes. Cereal Chem 76:558–565

    Article  Google Scholar 

  20. Jia JZ, Zhao SC, Kong XY, Li YR, Zhao GY et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95

    CAS  Article  PubMed  Google Scholar 

  21. Johansson A, Rasmussen SK, Harthill JE, Welinder KG (1992) cDNA, amino acid and carbohydrate sequence of barley seed-specific peroxidase BP 1. Plant Mol Biol 18:1151–1161

    CAS  Article  PubMed  Google Scholar 

  22. Kobrehel K, Feillet P (1975) Identification of genomes and chromosomes involved in peroxidase synthesis of wheat seeds. Can J Bot 53:2336–2344

    CAS  Article  Google Scholar 

  23. Kobrehel K, Laignelet B, Feillet P (1974) Study of some factors of macaroni brownness. Cereal Chem 51:675–684

    CAS  Google Scholar 

  24. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  25. Lagudah ES, Appels R, McNeil D (1991) The Nor-D3 locus of Triticum tauschii: natural variation and genetic linkage to markers in chromosome 5. Genome 34:387–395

    CAS  Article  Google Scholar 

  26. Li WL, Faris JD, Chittoor JM, Leach JE, Hulbert SH, Liu DJ, Chen PD, Gill BS (1999) Genomic mapping of defense response genes in wheat. Theor Appl Genet 98:226–233

    CAS  Article  Google Scholar 

  27. Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175:361–374

    PubMed Central  Article  PubMed  Google Scholar 

  28. Ling HQ, Zhao SC, Liu DC, Wang JY, Sun H, Zhang C, Fan HJ, Li D, Dong LL, Tao Y, Gao C, Wu HL, Li YW, Cui Y, Guo XS, Zheng SS, Wang B, Yu K, Liang QS, Yang WL, Lou XY, Chen J, Feng MJ, Jian JB, Zhang XF, Luo GB, Jiang Y, Liu JJ, Wang ZB, Sha YH, Zhang BR, Wu HJ, Tang DZ, Shen QH, Xue PY, Zou SH, Wang XJ, Liu X, Wang FM, Yang YP, An XL, Dong ZY, Zhang KP, Zhang XQ, Luo MC, Dvorak J, Tong YP, Wang J, Yang HM, Li ZS, Wang DW, Zhang AM, Wang J (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90

    CAS  Article  PubMed  Google Scholar 

  29. Liu YN, He ZH, Appels R, Xia XC (2012) Functional markers in wheat: current status and future prospects. Theor Appl Genet 125:1–10

    CAS  Article  PubMed  Google Scholar 

  30. Maksimov IV, Cherepanova EA, Kuzmina OI, Yarullina LG, Akhunov AA (2010) Molecular peculiarities of the chitin-binding peroxidases of plants. Russ J Bioorganic Chem 36:293–330

    CAS  Article  Google Scholar 

  31. Malosetti M, Ribaut JM, Vargas M, Crossa J, Eeuwijk FA (2008) A multi-trait multi-environment QTL mixed model with an application to drought and nitrogen stress trials in maize (Zea mays L.). Euphytica 161:241–257

    Article  Google Scholar 

  32. Matsuo RR, Dexter J (1980) Relationship between some durum wheat physical characteristics and semolina milling properties. Can J Plant Sci 60:49–53

    Article  Google Scholar 

  33. Morris CF (2002) Puroindolines: the molecular genetic basis of wheat grain hardness. Plant Mol Biol 48:633–647

    CAS  Article  PubMed  Google Scholar 

  34. Passardi F, Longet D, Penel C, Dunand C (2004) The class III peroxidase multigenic family in rice and its evolution in land plants. Phytochemistry 65:1879–1893

    CAS  Article  PubMed  Google Scholar 

  35. Peng JR, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261

    CAS  Article  PubMed  Google Scholar 

  36. Piontek K, Glumoff T, Winterhalter K (1993) Low pH crystal structure of glycosylated lignin peroxidase from Phanerochate chrysosporium at 2.5 Å resolution. FEBS Lett 315:119–124

    CAS  Article  PubMed  Google Scholar 

  37. Poulos TL, Patterson WR, Sundaramoorthy M (1995) The crystal structure of ascorbate and manganese peroxidase: the role of non-haem metal in the catalytic mechanism. Biochem Soc Trans 23:228–232

    CAS  Article  PubMed  Google Scholar 

  38. Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour P, Chalhoub B, Brunel D, Beckert M, Charmet G (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49:1131–1139

    CAS  Article  PubMed  Google Scholar 

  39. Revanappa SB, Salimath PV, Prasada Rao UJS (2014) Effect of peroxidase on textural quality dough and arabinoxylan characteristic isolated from whole wheat flour dough. Int J Food Microbiol 17:2131–2141

    CAS  Google Scholar 

  40. Rhee SG, Woo HA, Kil IS, Bae SH (2012) Peroxiredoxin functions as a peroxidase and a regulator and sensor of local peroxides. J Biol Chem 287:4403–4410

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  41. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    CAS  Article  Google Scholar 

  42. Taha SA, Sagi F (1987) Relationships between chemical composition of durum wheat semolina and macaroni quality. II. Ash, carotenoid pigments and oxidative enzymes. Cereal Res Commun 15:123–129

    CAS  Google Scholar 

  43. Takasaki S, Kato Y, Murata M, Homma S, Kawakishi S (2005) Effects of peroxidase and hydrogen peroxide on the dityrosine formation and the mixing characteristics of wheat-flour dough. Biosci Biotechnol Biochem 69:1686–1692

    CAS  Article  PubMed  Google Scholar 

  44. Theilade B, Rasmussen SK (1992) Structure and chromosomal localization of the gene encoding barley seed peroxidase BP 2A. Gene 118:261–266

    CAS  Article  PubMed  Google Scholar 

  45. Trono D, Pastore D, Di Fonzo N (1999) Carotenoid dependent inhibition of durum wheat lipoxygenase. J Cereal Sci 29:99–102

    CAS  Article  Google Scholar 

  46. Veldboom LR, Lee M (1996) Genetic mapping of quantitative trait loci in maize in stress and non-stress environments: I. Grain yield and yield components. Crop Sci 36:1310–1319

    CAS  Article  Google Scholar 

  47. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    CAS  Article  PubMed  Google Scholar 

  48. Wang SC, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, IWGSC, Lillemo M, Mather D, Appels R, Dolferus R, Guedira GB, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploidy wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  49. Yanagisawa T, Kiribuchi-Otobe C, Hirano H, Suzuki Y, Fujita M (2003) Detection of single nucleotide polymorphism (SNP) controlling the waxy character in wheat by using a derived cleaved amplified polymorphic sequence (dCAPS) marker. Theor Appl Genet 107:84–88

    CAS  PubMed  Google Scholar 

  50. Žilić S, Serpen A, Akillioğlu G, Janković M, Gőkmen V (2012) Distributions of phenolic compounds, yellow pigments and oxidative enzymes in wheat grains and their relation to antioxidant capacity of bran and debranned flour. J Cereal Sci 56:652–658

    Article  Google Scholar 

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The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This study was supported by the National Natural Science Foundation of China (31260327, 31461143021), the National 863 Project (2012AA10A308), the Gene Transformation Projects (2011ZX08009-003, 2011ZX08002004-008), International Science & Technology Cooperation Program of China (2014DFG31690), and China Agriculture Research System (CARS-3-1-3).

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Correspondence to Xianchun Xia.

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Wei, J., Geng, H., Zhang, Y. et al. Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL. Theor Appl Genet 128, 2067–2076 (2015).

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  • Quantitative Trait Locus
  • Common Wheat
  • Quantitative Trait Locus Analysis
  • Chinese Spring
  • Recombinant Inbred Line Population