title: Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study.
abstract: 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.
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Bartel
authors: B
authors: Vanholme
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Igor
authors: I
authors: Cesarino
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Geert
authors: G
authors: Goeminne
authors: Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA.
authors: Hoon
authors: H
authors: Kim
authors: Istituto di Genomica Applicata, 33100, Udine, Italy.
authors: Fabio
authors: F
authors: Marroni
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Rebecca
authors: R
authors: Van Acker
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Ruben
authors: R
authors: Vanholme
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Kris
authors: K
authors: Morreel
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Bart
authors: B
authors: Ivens
authors: Istituto di Genomica Applicata, 33100, Udine, Italy.
authors: Sara
authors: S
authors: Pinosio
authors: Istituto di Genomica Applicata, 33100, Udine, Italy.|Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100, Udine, Italy.
authors: Michele
authors: M
authors: Morgante
authors: Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA.
authors: John
authors: J
authors: Ralph
authors: INRA - Unité Amélioration, Génétique et Physiologie forestières, Olivet, France.
authors: Catherine
authors: C
authors: Bastien
authors: Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium.
authors: Wout
authors: W
authors: Boerjan
mesh_terms: D000217:Acyltransferases / Q000235:genetics*; D000483:Alleles; D001947:Breeding / Q000379:methods*; D002473:Cell Wall / Q000737:chemistry / Q000235:genetics; D006720:Homozygote; D008031:Lignin / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009154:Mutation; D032107:Populus / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012765:Shikimic Acid / Q000031:analogs & derivatives / Q000378:metabolism
chemical_list: C548291:4-coumaroylshikimic acid; D012765:Shikimic Acid; D008031:Lignin; D000217:Acyltransferases