Automation of DNA Marker Analysis for Molecular Breeding in Crops

  • Christophe DaytegEmail author
  • Stine Tuvesson


Plant breeders constantly need to adapt their research to the ever-changing market needs and agricultural practices. To achieve these goals, they need to competently combine different genetically-governed characters in a genotype, this is a complex, time-consuming and labour intensive task. In modern plant breeding, molecular markers are of increasing importance, and it is today undeniable that their application inhold tremendous possibilities to increase plant breeding efficiency. While the methods are more widely adopted, the capacity for high-throughput analyses at low cost becomes crucial for their practical use. To be attractive it is necessary that molecular technology is able to promptly handle sufficiently large amounts of material at reduced costs. Automation of the analysis processes is a way to meet these requirements. In that purpose, the specific needs of molecular applications in practical plant breeding are investigated in this chapter. The particular approach of a plant breeding company to automate them, in order to increase their availability to breeding programs, is described.


Genetically Modify Powdery Mildew Plant Breeding Barley Yellow Dwarf Virus Marker Technology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Formas and Øforsk are acknowledged for their financial support.


  1. Allard RW (1960) Principles of Plant Breeding. John Wiley, New YorkGoogle Scholar
  2. Bergal P, Friedberg L (1940) Essai d’identification des orges cultivées en France. Ann Epiphyt phytogenet VI:2–4Google Scholar
  3. Brandt DW (1998) Core system model: understanding the impact of reliability on high-throughput screening systems. Drug Discov Today 3(2):61–68CrossRefGoogle Scholar
  4. Cahill DJ, Schmidt DH (2004) Use of marker assisted selection in a product development breeding program. In: New directions for a diverse planet. Proceeding of the 4th International Crop Science Congress. Brisbane, AustraliaGoogle Scholar
  5. Chen S, Lin XH, Xu C et al (2000) Improvement of bacterial blight resistance ‘Minghui 63’ an elite restorer line of hybrid rice, by molecular marker-assisted selection. Crop Sci 40:239–244CrossRefGoogle Scholar
  6. Cheung WY, Hubert N, Landry BS (1993) A simple and rapid DNA microextraction method for plant, animal and insect suitable for RAPD and other PCR analyses. PCR Meth Appl 3:69–70Google Scholar
  7. Dayteg C (2008) Automation of molecular markers in practical breeding of spring barley (Hordeum vulgare L.). ISBN: 978-91-85913-31-2Google Scholar
  8. Dayteg C, Rasmussen M, Tuvesson S et al (2008) Development of an ISSR-derived PCR marker linked to nematode resistance (Ha2) in spring barley. Plant Breed 127:24–27CrossRefGoogle Scholar
  9. Dayteg C, Tuvesson S, Merker A et al (2007) Automation of DNA marker analysis for molecular breeding in crops: practical experience of a plant breeding company. Plant Breed 126:410–415CrossRefGoogle Scholar
  10. Dayteg C, von Post L, Öhlund R et al (1998) Quick DNA extraction method for practical plant breeding programmes. In: Plant and animal genome VI. San Diego, CAGoogle Scholar
  11. Dekkers JCM, Hospital F (2002) The use of molecular genetics in the improvement of agricultural populations. Nature 3:22–32Google Scholar
  12. Edwards KJ, Mogg R (2001) Plant genotyping by analysis of single nucleotide polymorphisms. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI, UKGoogle Scholar
  13. Fetch TGJ, Steffenson BJ, Nevo E (2003) Diversity and sources of multiple disease resistance in Hordeum spontaneum. Plant Dis 12:1439–1448CrossRefGoogle Scholar
  14. Frisch M, Bohn M, Melchinger AE (1998) Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci 39:1295–1301CrossRefGoogle Scholar
  15. Gupta PK, Varshney RK, Sharma PC et al (1999) Molecular markers and their applications in wheat breeding. Plant Breed 118:369–390CrossRefGoogle Scholar
  16. Helentjaris TG, King G, Slocum M et al (1985) Restriction fragment length polymorphism as probes for plant diversity and their developments as tools for applied plant breeding. Plant Mol Biol 5:109–118CrossRefGoogle Scholar
  17. Hernandez P (2004) Development and use of genomic tools for cereal introversion breeding. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation for plant breeding. Proceedings of the 17th EUCARPIA General Congress. BOKU, ViennaGoogle Scholar
  18. Holland JB (2004) Implementation of molecular markers for quantitative traits in breeding programs – challenges and opportunities. In: New directions for a diverse planet. Proceedings of the 4th International Crop Science Congress. Brisbane, AustraliaGoogle Scholar
  19. Hospital F (2003) Marker-assisted breeding. In: Newbury HJ (ed) Plant molecular breeding. Blackwell, UKGoogle Scholar
  20. Ivandic V, Walther U, Graner A (1998) Molecular mapping of a new gene in wild barley conferring complete resistance to leaf rust (Puccina hordei Otth). Theor Appl Genet 97:1235–1239CrossRefGoogle Scholar
  21. Jahoor A, Fischbeck G (1987) Sources of resistance to powdery mildew in barley lines derived from Hordeum spontaneum collected in Israel. Plant Breed 99:274–281CrossRefGoogle Scholar
  22. Klapper PE, Jungkind DL, Ferner T et al (1998) Multicenter international work flow study of an automated polymerase chain reaction instrument. Clin Chem 44:1737–1739PubMedGoogle Scholar
  23. Knapp SJ (1998) Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Sci 38:1164–1174CrossRefGoogle Scholar
  24. Koebner R (2003) MAS in cereals: Green for maize, amber for rice, still red for wheat and barley. In: Marker assisted selection: A fast track to increase genetic gain in plant and animal breeding? Session I: MAS in plants. Proceedings of an international workshop organised by the Fondazione per le Biotecnologie, the University of Turin and FAO. Turin, ItalyGoogle Scholar
  25. Kolodinska-Brantestam A, von Bothmer R, Dayteg C et al (2004) Inter simple sequence analysis of genetic diversity and relationships in cultivated barley of Nordic and Baltic origin. Hereditas 141:186–192CrossRefPubMedGoogle Scholar
  26. Kolodinska-Brantestam A, von Bothmer R, Rashal I et al (2006) Genetic diversity changes and relationships in spring barley germplasm of Nordic and Baltic areas as shown by SSR markers. Genet Resour Crop Ev 54:749–758CrossRefGoogle Scholar
  27. Korzun V (2003) Molecular markers and their applications in cereals breeding. In Marker assisted selection: A fast track to increase genetic gain in plant and animal breeding? Session I: MAS in plants. Proceedings of an international workshop organised by the Fondazione per le Biotecnologie, the University of Turin and FAO. Turin, ItalyGoogle Scholar
  28. Liu BH, Knapp SJ (1990) GMENDEL: A program for Mendelian segregation and linkage analysis of individual and multiple progeny populations using log-likelihood ratios. J Hered 81:407Google Scholar
  29. Lombard V, Baril CP, Dubreuil P et al (2000) Genetic relationships and fingerprinting of rapeseed cultivars by AFLP: Consequences for varietal registration. Crop Sci 40:1417–1425CrossRefGoogle Scholar
  30. Lydiate D (1999) Saskatoon genomics initiative could revolutionize canola research. The Agbiotech bulletinGoogle Scholar
  31. Ma C, Fu T, Bengtsson L et al (2003) Genetic diversity of Chinese and Swedish Brassica napus cultivars based on Inter-SSR PCR markers and its relationship to hybrid performance. J Swed Seed Assoc 2:67–77Google Scholar
  32. Mace ES, Buhariwalla HK, Crouch JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Rep 21:459a–459hCrossRefGoogle Scholar
  33. Melchinger AE (1990) Use of molecular markers in breeding for oligogenic disease resistance. Plant Breed 104:1–19CrossRefGoogle Scholar
  34. Nilsson-Ehle H (1914) Zur Kentnis der mit der Keimungsphysiologie des Weizens in Zusammenhang stehenden innerern Faktoren. Z Pflanzenzuecht 2:153–157Google Scholar
  35. Ordon F, Weyen J, Korell M et al (1996) Exotic barley germplasms in breeding for resistance to soil-borne viruses. Euphytica 92:275–280CrossRefGoogle Scholar
  36. Peleman JD, van der Voort JR (2003) The challenges in marker assisted breeding. In: van Hintum ThJL, Lebeda A, Pink DA, Schut JW (eds) Eucarpia leafy vegetables. CGN, WageningenGoogle Scholar
  37. Ribaut J-M, Bertrán J (1999) Single large-scale marker-assisted selection (SLS-MAS). Mol Breed 5:531–541CrossRefGoogle Scholar
  38. Saiki RK, Gelfand DH, Stoffel S et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491CrossRefPubMedGoogle Scholar
  39. Sorrells ME, William WA (1997) Direct classification and selection of superior alleles for crop improvement. Crop Sci 37:691–697CrossRefGoogle Scholar
  40. Tanksley SD, Rick CM (1980) Isozymic gene linkage map of the tomato: applications in genetics and breeding. Theor Appl Genet 57:161–170CrossRefGoogle Scholar
  41. Tuvesson S, Dayteg C, Hagberg P et al (2007) Molecular markers and doubled haploids in European plant breeding. Euphytica 158:278–294CrossRefGoogle Scholar
  42. Tuvesson S, von Post L, Öhlund R et al (1998) Molecular breeding for the BaMMV/BaYMV resistance gene ym4 in winter barley. Plant Breed 117:19–22CrossRefGoogle Scholar
  43. Werner K, Friedt W, Ordon F (2005) Strategies for pyramiding resistance genes against the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2). Mol Breed 16:45–55CrossRefGoogle Scholar
  44. Villanueva B, Pong-Wong R, Williams JA (2002) Marker assisted selection with optimised contributions of the candidates to selection. Gen Sel Evol 34:679–703CrossRefGoogle Scholar
  45. von Post R, von Post L, Dayteg C et al (2003) A high-throughput DNA extraction method for barley seed. Euphytica 130:255–260CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Department of Plant Breeding and BiotechnologySwedish University of Agricultural SciencesAlnarpSweden
  2. 2.Svalöf Weibull AB, SW LaboratorySvalövSweden

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