Theoretical and Applied Genetics

, Volume 132, Issue 12, pp 3375–3398 | Cite as

Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits

  • Pernille L. Malik
  • Luc Janss
  • Linda K. Nielsen
  • Finn Borum
  • Henning Jørgensen
  • Birger Eriksen
  • Jan K. Schjoerring
  • Søren K. RasmussenEmail author
Original Article


Key message

This study demonstrates that an active breeding nursery with rotation can be used to identify marker–trait associations for biomass yield and quality parameters that are important for biorefinery purposes.


Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013–2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker–trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10−6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.



We thank Morten Læssøe Stephensen from the University of Copenhagen and Ole Andersen, Erling and Helle Hisselholm, and other employees at Sejet Plant Breeding A/S for their help with plant harvests and the recording of phenotypic data. Britta Skov and Anja Hecht Ivø of the University of Copenhagen are acknowledged for their technical support with the laboratory analyses. The project was funded by Sejet Plant Breeding A/S and Innovation Fund Denmark, Grant 12-132625 (biovalue: value-added products from biomass to J.K.S.).

Author contribution statement

PLM, JKS, BE and SKR conceived and designed the experiments; LKN, FB and BE designed and carried out the field experiments, conducted phenotyping and provided SNP marker data; PLM performed all the experiments; PLM analysed the data with the contribution of LJ; PLM drafted and finalized the article with writing contributions from all the authors; the final article was approved by all the authors.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed consent

Not applicable.

Supplementary material

122_2019_3431_MOESM1_ESM.docx (582 kb)
Supplementary material 1 (DOCX 582 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
  2. 2.Department of Molecular Biology and GeneticsAarhus UniversityTjeleDenmark
  3. 3.Sejet Plant BreedingHorsensDenmark

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