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Breeding with defective alleles

Breeding with rare defective alleles (BRDA)

IGA has used NGS to detect mutations in five genes for lignin biosynthesis in 768 trees of black poplar, sampled in forests from across Western Europe in France, Italy, Germany, Spain, and The Netherlands. A total of 36 non-synonymous single nucleotide polymorphisms were identified. The rarest validated variant was estimated to occur only once in 1536 chromosomes.

One mutation causes a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The mutant allele encodes a truncated protein. One naturally occurring poplar tree is homozygous for this recessive allele and its lignin composition is 17-fold enriched in p-hydroxyphenyl units, compared to trees that encode the full-length HCT1 enzyme.

This proof-of-concept in poplar led us to propose a breeding strategy, called 'breeding with rare defective alleles' (BRDA), as a tool for conventional breeding based on the capture of rare defective alleles from wild germplasm. Naturally occurring variants are identified in wild populations and their rare useful alleles are introduced into the breeding germplasm.

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 198:765-776