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

Bartel Vanholme (UGent) , Igor Cesarino (UGent) , Geert Goeminne (UGent) , Hoon Kim, Fabio Marroni, Rebecca Van Acker (UGent) , Ruben Vanholme (UGent) , Kris Morreel (UGent) , Bart Ivens (UGent) , Sara Pinosio, et al.
(2013) NEW PHYTOLOGIST. 198(3). p.765-776
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Biotechnology for a sustainable economy (Bio-Economy)
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, PnHCT-1-Delta 73, 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.
Keywords
LOBLOLLY PINE, CINNAMYL ALCOHOL DEHYDROGENASE, shikimate, poplar, p-hydroxyphenyl, natural population, lignin, EcoTILLING, Breeding with rare defective alleles (BRDA), ARABIDOPSIS THALIANA, DOWN-REGULATION, MONOMER COMPOSITION, GENETIC ANALYSIS, FORAGE QUALITY, FOREST TREES, BIOSYNTHESIS, CLONING

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Chicago
Vanholme, Bartel, Igor Cesarino, Geert Goeminne, Hoon Kim, Fabio Marroni, Rebecca Van Acker, Ruben Vanholme, et al. 2013. “Breeding with Rare Defective Alleles (BRDA): a Natural Populus Nigra HCT Mutant with Modified Lignin as a Case Study.” New Phytologist 198 (3): 765–776.
APA
Vanholme, B., Cesarino, I., Goeminne, G., Kim, H., Marroni, F., Van Acker, R., Vanholme, R., et al. (2013). Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. NEW PHYTOLOGIST, 198(3), 765–776.
Vancouver
1.
Vanholme B, Cesarino I, Goeminne G, Kim H, Marroni F, Van Acker R, et al. Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. NEW PHYTOLOGIST. 2013;198(3):765–76.
MLA
Vanholme, Bartel, Igor Cesarino, Geert Goeminne, et al. “Breeding with Rare Defective Alleles (BRDA): a Natural Populus Nigra HCT Mutant with Modified Lignin as a Case Study.” NEW PHYTOLOGIST 198.3 (2013): 765–776. Print.
@article{4145887,
  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, PnHCT-1-Delta 73, 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.},
  author       = {Vanholme, Bartel and Cesarino, Igor and Goeminne, Geert and Kim, Hoon and Marroni, Fabio and Van Acker, Rebecca and Vanholme, Ruben and Morreel, Kris and Ivens, Bart and Pinosio, Sara and Morgante, Michele and Ralph, John and Bastien, Catherine and Boerjan, Wout},
  issn         = {1469-8137},
  journal      = {NEW PHYTOLOGIST},
  keyword      = {LOBLOLLY PINE,CINNAMYL ALCOHOL DEHYDROGENASE,shikimate,poplar,p-hydroxyphenyl,natural population,lignin,EcoTILLING,Breeding with rare defective alleles (BRDA),ARABIDOPSIS THALIANA,DOWN-REGULATION,MONOMER COMPOSITION,GENETIC ANALYSIS,FORAGE QUALITY,FOREST TREES,BIOSYNTHESIS,CLONING},
  language     = {eng},
  number       = {3},
  pages        = {765--776},
  title        = {Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study},
  url          = {http://dx.doi.org/10.1111/nph.12179},
  volume       = {198},
  year         = {2013},
}

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