1932

Abstract

Extrachromosomal DNA such as organelle DNA are increasingly targeted in molecular detection assays where samples have been degraded by physical or chemical means. Owing to multiple organelles per cell and greater copy numbers than nuclear genes, organelle gene targets provide a more robust signal in polymerase chain reaction (PCR), quantitative PCR (qPCR), and other emerging molecular technologies. Because of these advantages, direct analysis of organelle DNA in food matrices is used for detection of contaminants and identification and authentication of food ingredients and allergens. Non-nuclear DNA is also used as an assay normalizer for detection of genetically modified organisms (GMOs) in foods. This review describes these protocols plus the effects of processing on efficacy, with special emphasis on thermally produced DNA fragmentation. Future research may incorporate molecular techniques beyond detection, used instead as time-temperature indicators in thermal food processing or quality indicators in food fermentation or acidification.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-food-030216-030216
2017-02-28
2024-10-10
Loading full text...

Full text loading...

/deliver/fulltext/food/8/1/annurev-food-030216-030216.html?itemId=/content/journals/10.1146/annurev-food-030216-030216&mimeType=html&fmt=ahah

Literature Cited

  1. Aida AA, Che Man YB, Wong CMVL, Raha AR, Son R. 2005. Analysis of raw meats and fats of pigs using polymerase chain reaction for Halal authentication. Meat Sci 69:47–52 [Google Scholar]
  2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. 2002. The genetic systems of mitochondria and plastids. Molecular Biology of the Cell New York: Garland Science, 4th ed.. [Google Scholar]
  3. Ali ME, Hashim U, Mustafa S, Che Man YB, Dhahi TS. et al. 2012. Analysis of pork adulteration in commercial meatballs targeting porcine-specific mitochondrial cytochrome b gene by TaqMan probe real-time polymerase. Meat Sci 91:454–59 [Google Scholar]
  4. Andreasson H, Gyllensten U, Allen M. 2002. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. BioTechniques 33:2402–11 [Google Scholar]
  5. Arslan A, Ilhak I, Calicioglu M. 2006. Effect of method of cooking on identification of heat processed beef using polymerase chain reaction (PCR) technique. Meat Sci 72:326–30 [Google Scholar]
  6. Aslan O, Hamill RM, Sweeney T, Reardon W, Mullen AM. 2009. Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: implications for food traceability. J. Anim. Sci. 87:57–61 [Google Scholar]
  7. Barrett TJ, Gerner-Smidt P. 2007. Molecular source tracking and molecular subtyping. Food Microbiology: Fundamentals and Frontiers MP Doyle, LR Beuchat 987–1004 Washington, DC: ASM Press, 3rd ed.. [Google Scholar]
  8. Bauer T, Hammes WP, Haase NU, Hertel C. 2004. Effect of food components and processing parameters on DNA degradation in food. Environ. Biosaf. Res. 3:215–23 [Google Scholar]
  9. Bauer T, Weller P, Hammes WP, Hertel C. 2003. The effect of processing parameters on DNA degradation in food. Eur. Food Res. Technol. 217:338–43 [Google Scholar]
  10. Bellagamba F, Moretti V, Comincini S, Valfre F. 2001. Identification of species in animal feedstuffs by polymerase chain reaction-restriction fragment length polymorphism analysis of mitochondrial DNA. J. Agric. Food Chem. 49:3775–81 [Google Scholar]
  11. Bosmali I, Ganopoulos I, Madesis P, Tsaftaris A. 2012. Microsatellite and DNA-barcode regions typing combined with High Resolution Melting (HRM) analysis for food forensic uses: A case study on lentils (Lens culinaris). Food Res. Int. 46:141–47 [Google Scholar]
  12. Brezna B, Hudecova L, Kuchta T. 2006. Detection of pea in food by real-time polymerase chain reaction (PCR). Eur. Food Res. Technol. 222:600–3 [Google Scholar]
  13. Brodmann PD, Moor D. 2003. Sensitive and semi-quantitative TaqMan real-time polymerase chain reaction systems for the detection of beef (Bos Taurus) and the detection of the family Mammalia in food and feed. Meat Sci 65:599–607 [Google Scholar]
  14. Busconi M, Foroni C, Corradi M, Bongiorni C, Cattapan F, Fogher C. 2003. DNA extraction from olive oil and its use in the identification of the production cultivar. Food Chem 83:127–34 [Google Scholar]
  15. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J. et al. 2009. The MIQE Guidelines: Minimum Information for publication of Quantitative real-time PCR Experiments. Clin. Chem. 55:611–22 [Google Scholar]
  16. Caldwell JM, Perez-Diaz IM, Harris K, Hassan HM, Simunovic J, Sandeep KP. 2015a. Mitochondrial DNA fragmentation to monitor processing parameters in high acid, plant-derived foods. J. Food Sci. 80:M2892–98 [Google Scholar]
  17. Caldwell JM, Perez-Diaz IM, Harris K, Hendrix K, Sanders TH. 2016. Mitochondrial DNA fragmentation to monitor safety and quality in roasted peanuts. J. Peanut Sci. 43:1–12 [Google Scholar]
  18. Caldwell JM, Perez-Diaz IM, Sandeep KP, Simunovic J, Harris K. et al. 2015b. Mitochondrial DNA fragmentation as a molecular tool to monitor thermal processing of plant-derived, low-acid foods, and biomaterials. J. Food Sci. 80:M1804–14 [Google Scholar]
  19. Che Man YB, Aida AA, Raha AR, Son R. 2007. Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) of Halal verification. Food Control 18:885–89 [Google Scholar]
  20. Chen Y, Ge YQ, Wang Y. 2007. Effect of critical processing procedures on transgenic components in quality and quantity level during soymilk processing of Roundup Ready soybean. Eur. Food Res. Technol. 225:119–26 [Google Scholar]
  21. Dalmasso A, Fontanella E, Piatti P, Civera T, Rosati S, Bottero MT. 2004. A multiplex PCR assay for the identification of animal species in foodstuffs. Mol. Cell. Probes 18:81–87 [Google Scholar]
  22. Debode F, Janssen E, Berben G. 2007. Physical degradation of genomic DNA of soybean flours does not impair relative quantification of its transgenic content. Eur. Food Res. Technol. 226:273–80 [Google Scholar]
  23. Debode F, Marien A, Janssen E, Berben G. 2010. Design of multiplex calibrant plasmids, their use in GMO detection and the limit of their applicability for quantitative purposes owing to competition effects. Anal. Bioanal. Chem. 396:2151–64 [Google Scholar]
  24. Demirhan Y, Ulca P, Senyuva HZ. 2012. Detection of porcine DNA in gelatine and gelatine-containing processed food products—Halal/Kosher authentication. Meat Sci 90:686–89 [Google Scholar]
  25. Doktycz MJ. 1997. Nucleic acids: thermal stability and denaturation. eLS doi: 10.1038/npg.els.0003123 [Google Scholar]
  26. Ehlert A, Demmel A, Hupfer C, Busch U, Engel KH. 2009. Simultaneous detection of DNA from 10 food allergens by ligation-dependent probe amplification. Food Addit. Contam. 26:409–18 [Google Scholar]
  27. Faria MA, Magalhaes R, Ferreira MA, Meredith CP, Monteiro FF. 2000. Vitis vinifera must varietal authentication using microsatellite DNA analysis (SSR). J. Agric. Food Chem. 48:1096–100 [Google Scholar]
  28. Feng P. 2007. Rapid methods for the detection of foodborne pathogens: current and next-generation technologies. Food Microbiology: Fundamentals and Frontiers MP Doyle, LR Beuchat 911–34 Washington, DC: ASM Press, 3rd ed.. [Google Scholar]
  29. Galimberti A, De Mattia F, Losa A, Bruni I, Federici S. et al. 2013. DNA barcoding as a new tool for food traceability. Food Res. Int. 50:55–63 [Google Scholar]
  30. Gerber AS, Loggins R, Kumar S, Dowling TE. 2001. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?. Annu. Rev. Genet. 35:539–66 [Google Scholar]
  31. Goncalves J, Pereira F, Amorim A, van Asch B. 2012. New method for the simultaneous identification of cow, sheep, goat, and water buffalo in dairy products by analysis of short species-specific mitochondrial DNA targets. J. Agric. Food Chem. 60:10480–85 [Google Scholar]
  32. Gryson N. 2010. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review. Anal. Bioanal. Chem. 396:2003–22 [Google Scholar]
  33. Handa H. 2003. The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and. Arabidopsis thaliana. Nucleic Acids Res 31:5907–16 [Google Scholar]
  34. Haye PA, Segovia NI, Vera R, de los Angeles Gallardo M, Gallardo-Escarate C. 2012. Authentication of commercialized crab-meat in Chile using DNA barcoding. Food Control 25:239–44 [Google Scholar]
  35. Herman L. 1997. Detection of viable and dead Listeria monocytogenes by PCR. Food Microbiol 14:103–10 [Google Scholar]
  36. Hird H, Chisholm J, Sanchez A, Hernandez M, Goodier R. et al. 2006. Effect of heat and pressure processing on DNA fragmentation and implications for the detection of meat using a real-time polymerase chain reaction. Food Addit. Contam. 23:645–50 [Google Scholar]
  37. Hopwood AJ, Fairbrother KS, Lockley AK, Bardsley RG. 1999. An actin gene-related polymerase chain reaction (PCR) test for identification of chicken in meat mixtures. Meat Sci 53:227–31 [Google Scholar]
  38. Horreo JL, Ardura A, Pola IG, Martinez JL, Garcia-Vazquez E. 2013. Universal primers for species authentication of animal foodstuff in a single polymerase chain reaction. J. Sci. Food Agric. 93:354–61 [Google Scholar]
  39. Hrnĉírová Z, Bergerová E, Siekel P. 2008. Effects of technological treatment on DNA degradation in selected food matrices of plant origin. J. Food Nutr. Res. 47:23–28 [Google Scholar]
  40. James D, Schmidt A-M. 2004. Use of an intron region of a chloroplast tRNA gene (trnL) as a target for PCR identification of specific food crops including sources of potential allergens. Food Res. Int. 37:395–402 [Google Scholar]
  41. Kharazmi M, Bauer T, Hammes WP, Hertel C. 2003. Effect of food processing on the fate of DNA with regard to degradation and transformation capability in Bacillus subtilis. Syst. Appl. Microbiol. 26:495–501 [Google Scholar]
  42. Keim SA, Kulkarni MM, McNamara K, Geraghty SR, Billock RM, Ronau R. et al. 2015. Cow's milk contamination of human milk purchased via the internet. Pediatrics 135:e1157–62 [Google Scholar]
  43. Kesman Z, Gulluce A, Sahin F, Yetim H. 2009. Identification of meat species by TaqMan-based real-time PCR assay. Meat Sci 82:444–49 [Google Scholar]
  44. Kesman Z, Sahin F, Yetim H. 2007. PCR assay for the identification of animal species in cooked sausages. Meat Sci 77:649–53 [Google Scholar]
  45. Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709–15 [Google Scholar]
  46. Lee JH, Lee JW, Sung JS, Bang KH, Moon SG. 2009. Molecular authentication of 21 Korean Artemisia species (Compositae) by polymerase chain reaction-restriction fragment length polymorphism based on trnL-F region of chloroplast DNA. Biol. Pharm. Bull. 32:1912–16 [Google Scholar]
  47. Lin W-F, Hwang D-F. 2007. Application of PCR-RFLP analysis on species identification of canned tuna. Food Control 18:1050–57 [Google Scholar]
  48. Lipp M, Brodmann P, Pietsch K, Pauwels J, Anklam E. et al. 1999. IUPAC collaborative trial study of a method to detect genetically modified soy beans and maize in dried powder. J. AOAC Int. 82:923–28 [Google Scholar]
  49. Mane BG, Mendiratta SK, Tiwari AK. 2009. Polymerase chain reaction assay for identification of chicken in meat and meat products. Food Chem 116:806–10 [Google Scholar]
  50. Mane BG, Mendiratta SK, Tiwari AK. 2012. Beef specific polymerase chain reaction assay for authentication of meat and meat products. Food Control 28:246–49 [Google Scholar]
  51. Martin I, Garcia T, Fajardo V, Lopez-Calleja I, Rojas M. et al. 2007. Mitochondrial markers for the detection of four duck species and the specific identification of Muscovy duck in meat mixtures using the polymerase chain reaction. Meat Sci 76:721–29 [Google Scholar]
  52. Martinez C, Cosgaya P, Vasquez C, Gac S, Ganga A. 2007. High degree of correlation between molecular polymorphism and geographic origin of wine yeast strains. J. Appl. Microbiol. 103:2185–95 [Google Scholar]
  53. Maskova E, Paulickova I, Rysova J, Gabrovska D. 2011. Evidence for wheat, rye, and barley presence in gluten free foods by PCR method: comparison with ELISA method. Czech J. Food Sci. 29:45–50 [Google Scholar]
  54. Meyer R. 1999. Development and application of DNA analytical methods for the detection of GMOs in foods. Food Control 10:391–99 [Google Scholar]
  55. Moreano F, Busch U, Engel K-H. 2005. Distortion of genetically modified organism quantification in processed foods: influence of particle size compositions and heat-induced DNA degradation. J. Agric. Food Chem. 53:9971–79 [Google Scholar]
  56. Murray SR, Butler RC, Hardacre AK, Timmerman-Vaughan GM. 2007. Use of quantitative real-time PCR to estimate maize endogenous DNA degradation after cooking and extrusion or in food products. J. Agric. Food Chem. 55:2231–39 [Google Scholar]
  57. Murugaiah C, Noor ZM, Mastakim M, Bilung LM, Selamat J, Radu S. 2009. Meat species identification and Halal authentication analysis using mitochondrial DNA. Meat Sci 83:57–61 [Google Scholar]
  58. Pardo MA, Perez-Villareal B. 2004. Identification of commercial canned tuna species by restriction site analysis of mitochondrial DNA products obtained by nested primer PCR. Food Chem 86:143–50 [Google Scholar]
  59. Rahman MM, Ali ME, Hamid SBA, Mustafa S, Hashim U, Hanapi UK. 2014. Polymerase chain reaction assay targeting cytochrome b gene for the detection of dog meat adulteration in meatball formulation. Meat Sci 97:404–9 [Google Scholar]
  60. Ramos-Gomez S, Busto MD, Albillos SM, Ortega N. 2016. Novel qPCR systems for olive (Olea europaea L.) authentication in oils and foods. Food Chem 194:447–54 [Google Scholar]
  61. Rastogi G, Dharne MS, Walujkar S, Kumar A, Patole MS, Shouche YS. 2007. Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat Sci 76:666–74 [Google Scholar]
  62. Rojas M, Gonzalez I, Pavon MA, Pegels N, Hernandez PE. et al. 2011. Mitochondrial and nuclear markers for the authentication of partridge meat and the specific identification of red-legged partridge meat products by polymerase chain reaction. Poultry Sci 90:211–22 [Google Scholar]
  63. Sakalar E, Abasiyanik MF, Bektik E, Tayyrov A. 2012. Effect of heat processing on DNA quantification of meat species. J. Food Sci. 77:N40–44 [Google Scholar]
  64. Sambrook J, Russel D. 2001. Molecular Cloning: A Laboratory Manual New York: Cold Spring Harb. Lab. Press, 3rd ed.. [Google Scholar]
  65. Sforza S, Corradini R, Tedeschi T, Marchelli R. 2011. Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies. Chem. Soc. Rev. 40:221–32 [Google Scholar]
  66. Soares S, Amaral J, Mafra I, Beatriz M, Oliveira PP. 2010. Quantitative detection of poultry meat adulteration with pork by a duplex PCR assay. Meat Sci 85:531–36 [Google Scholar]
  67. Stamoulis P, Stamatis C, Sarafidou T, Mamuris Z. 2010. Development and application of molecular markers for poultry meat identification in food chain. Food Control 21:1061–65 [Google Scholar]
  68. Suyama T, Kawaharasaki M. 2013. Decomposition of waste DNA with extended autoclaving under unsaturated steam. BioTechniques 55:296–99 [Google Scholar]
  69. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C. et al. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14 [Google Scholar]
  70. Taylor RW, Turnbull DM. 2005. Mitochondrial DNA mutations in human disease. Nat. Rev. Genet. 6:390 [Google Scholar]
  71. Terio V, Di Pinto P, Decaro N, Parisi A, Desario C. et al. 2010. Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences. Mol. Cell. Probes 24:352–56 [Google Scholar]
  72. Trantakis IA, Spaniolas S, Kalaitzis P, Ioannou PC, Tucker GA, Christopoulos TK. 2012. Dipstick test for DNA-based food authentication. Application to coffee authenticity assessment. J. Agric. Food Chem. 60:713–17 [Google Scholar]
  73. Unseld M, Beyerman B, Brandt P, Hiesel R. 1995. Identification of the species origin of highly processed meat products by mitochondrial DNA sequences. Genome Res 4:241–43 [Google Scholar]
  74. Urdiain M, Domenech-Sanchez A, Alberti S, Benedi VJ, Rossello JA. 2005. New method of DNA isolation from two food additives suitable for authentication in polymerase chain reaction assays. J. Agric. Food Chem. 53:3345–47 [Google Scholar]
  75. van Asch B, Santos LS, Carneiro J, Pereira F, Amorim A. 2011. Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products. J. Agric. Food Chem. 59:6920–26 [Google Scholar]
  76. Watanabe T, Akiyama H, Maleki S, Yamakawa H, Iijima K. et al. 2006. A specific qualitative detection method for peanut (Arachis hypogaea) in food using polymerase chain reaction. J. Food Biochem. 30:215–33 [Google Scholar]
  77. Wolf C, Burgener M, Hubner P, Luthy J. 2000. PCR-RFLP analysis of mitochondrial DNA: differentiation of fish species. Lebensm.-Wiss. Technol. 33:144–50 [Google Scholar]
  78. Woolfe M, Primrose S. 2004. Food forensics: using DNA technology to combat misdescription and fraud. Trends Biotechnol 22:222–26 [Google Scholar]
  79. Xu W, Reuter T, Xu Y, Alexander TW, Gilroyed B. et al. 2009. Use of quantitative and conventional PCR to assess biodegradation of bovine and plant DNA during cattle mortality composting. Environ. Sci. Technol. 43:6248–55 [Google Scholar]
/content/journals/10.1146/annurev-food-030216-030216
Loading
/content/journals/10.1146/annurev-food-030216-030216
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error