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Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study

  1. Bartel Vanholme1,2,
  2. Igor Cesarino1,2,
  3. Geert Goeminne1,2,
  4. Hoon Kim3,
  5. Fabio Marroni4,
  6. Rebecca Van Acker1,2,
  7. Ruben Vanholme1,2,
  8. Kris Morreel1,2,
  9. Bart Ivens1,2,
  10. Sara Pinosio4,
  11. Michele Morgante4,5,
  12. John Ralph3,
  13. Catherine Bastien6,
  14. Wout Boerjan1,2,*

Article first published online: 25 FEB 2013

DOI: 10.1111/nph.12179

Issue

New Phytologist

New Phytologist

Volume 198, Issue 3, pages 765–776, May 2013

Additional Information

How to Cite

Vanholme, B., Cesarino, I., Goeminne, G., Kim, H., Marroni, F., Van Acker, R., Vanholme, R., Morreel, K., Ivens, B., Pinosio, S., Morgante, M., Ralph, J., Bastien, C. and Boerjan, W. (2013), Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. New Phytologist, 198: 765–776. doi: 10.1111/nph.12179

Author Information

  1. 1

    Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium

  2. 2

    Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium

  3. 3

    Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA

  4. 4

    Istituto di Genomica Applicata, Udine, Italy

  5. 5

    Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, Udine, Italy

  6. 6

    INRA – Unité Amélioration, Génétique et Physiologie forestières, Olivet, France

* Author for correspondence:
Wout Boerjan
Tel: +32 (0)9 33 13 881
Email: wout.boerjan@psb.vib-ugent.be

Publication History

  1. Issue published online: 12 APR 2013
  2. Article first published online: 25 FEB 2013
  3. Manuscript Accepted: 2 JAN 2013
  4. Manuscript Received: 15 NOV 2012

Funded by

  • European Commission within the Seventh Framework Programme for Research. Grant Number: FP7
  • ENERGYPOPLAR. Grant Number: FP7-211917
  • NOVELTREE. Grant Number: 211868
  • Bijzonder Onderzoeksfonds-Zware Apparatuur of the Ghent University. Grant Number: 174PZA05
  • Hercules Foundation. Grant Number: AUGE/014
  • U.S. Department of Energy's Great Lakes Bioenergy Research Center. Grant Number: BER DE–FC02–07ER64494
  • Multidisciplinary Research Partnership Ghent Bio-Economy

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Keywords:

  • Breeding with rare defective alleles (BRDA);
  • EcoTILLING;
  • lignin;
  • natural population;
  • p-hydroxyphenyl;
  • poplar;
  • shikimate

Summary

  • Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis.
  • The lignin composition of P. nigra trees homozygous for the defective allele was compared with that of heterozygous trees and trees without the defective allele. The lignin was characterized by phenolic profiling, lignin oligomer sequencing, thioacidolysis and NMR. In addition, HCT1 was heterologously expressed for activity assays and crosses were made to introduce the mutation in different genetic backgrounds.
  • HCT1 converts p-coumaroyl-CoA into p-coumaroyl shikimate. The mutant allele, PnHCT1-Δ73, encodes a truncated protein, and trees homozygous for this recessive allele have a modified lignin composition characterized by a 17-fold increase in p-hydroxyphenyl units.
  • Using the lignin pathway as proof of concept, we illustrated that the capture of rare defective alleles is a straightforward approach to initiate reverse genetics and accelerate tree breeding. The proposed breeding strategy, called ‘breeding with rare defective alleles’ (BRDA), should be widely applicable, independent of the target gene or the species.
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