Mutational mechanisms

Phenotypic variation within a cultivated species may arise from a multitude of genetic mechanisms. Fruit colour is one of the most conspicuous plant traits that attract human attention. Thus, genetic mutations that alter genes involved in fruit pigmentation are more frequently retained than mutations in any other trait. Unsurprisingly, sequencing of fruit colour variants reveals genetic architecture and mutational mechanisms of unexpected complexity.

Yellow fleshed peach

The degradation of carotenoids causes the peach flesh to exhibit white colour. Loss-of-function variants at a gene encoding the carotenoid cleavage dioxygenase 4 (PpCCD4) account for the difference between white and yellow fleshed varieties. Yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions. All these mutations, despite being located within the transcribed portion of the gene, resulted in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a plant gene for which humans, in their quest to diversify fruit appearance and qualitative characteristics of food, unconsciously selected multiple mutations resulting from a variety of mechanisms.

Falchi et al (2013) Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. Plant Journal 76(2):175-187