, Volume 175, Issue 1, pp 51-64

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

The role of molecular markers and marker assisted selection in breeding for organic agriculture

  • E. T. Lammerts van BuerenAffiliated withWageningen UR Plantbreeding, Wageningen University Email author 
  • , G. BackesAffiliated withFaculty of Life Sciences, Department of Agriculture and Ecology, University of Copenhagen
  • , H. de VriendAffiliated withLIS Consult
  • , H. ØstergårdAffiliated withRisø National Laboratory For Sustainable Energy, Biosystem Division, Technical University of Denmark DTU


Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/or conventional agriculture, such as the increasing competition and cost investments to get access to marker technology, and the need for bridging the gap between phenotyping and genotyping especially with complex and quantitative inherited traits such as nutrient-efficiency. A major conclusion of the authors is that more interaction and mutual understanding between organic and molecular oriented breeders is necessary and can benefit both research communities.


Organic agriculture Organic plant breeding Evaluation of molecular markers Marker assisted selection SWOT analysis Low-input agriculture