In ornamental crops the development of genetic and molecular tools for breeding has been slow because of the large number of ornamental species, many of which are genetically complicated for breeding, being outbreeding crops, polyploid, and/or having a large genome.
This is changing due to three recent developments: (i) next-generation sequencing can now generate large numbers of single nucleotide polymorphism (SNP) markers based on genomic or transcriptomic sequences, (ii) efficient and automated SNP detection systems render genotyping into an automated and relatively cheap process, and (iii) methods and software now exist to analyse these data, also in polyploid crops, to find associations with traits and to generate tools for marker-assisted breeding. The challenge for the coming years will be to implement these tools to speed up breeding.
When more genome sequences of ornamental species or related species become available, it will also be possible to move from associated markers (for a trait or QTL region) to the underlying variation in the causal genes. Knowledge of the existing variation in functional alleles will make it possible to consider directing biosynthetic or regulatory pathways towards, e.g. different colour or scent combinations.
New plant breeding techniques (also called ‘precision breeding techniques’) add new possibilities to direct the breeding process. Notably, gene editing (also called genome editing) using Crispr/Cas may be used to increase the pool of functional variation, but there are challenges to apply it in ornamentals, in terms of the availability of sequence information for the candidate genes and the existence of transformation and regeneration protocols.