Mutation rate and gene expression in genetic admixtures of domesticated citrus

Resumen

Citrus domestication is a largely unknown process. Research carried out to date indicates that current commercial citrus varieties are, in general, the product of ancestral intraspecific and interspecific introgressions. Intraspecific introgressions took place between the populations of two antique subspecies of mandarins and contributed to the apomictic behavior that most current mandarins and other related citrus still retain today. Once these genetic admixtures were established, interspecific pummelo introgression brought new traits to the admixtured mandarin genome. During domestication, genetic variability of these citrus occurred mainly through spontaneous mutations and with the practice of grafting, seedless genotypes expanded rapidly, emphasizing the role of mutations in the selection of citrus such as oranges and modern mandarins. In this work, we provide evidence that somatic mutations in citrus propagate following an iterative pattern determined by the sympodial branching model and consequently are grouped in sectors along the tree, where some of them remain fixed. In this scenario, a tree can be considered a mosaic genetically composed of different genomes, in which younger branches accumulate greater number of mutations. On average, our 36-yr-old experimental Clementine tree shows a mutation rate of 4.4 × 10-10 bp-1 yr-1, may carry a total of 1,500 to 5,000 variants and produces 1 somatic mutation per axillary meristem. This relatively high number of mutations is in line with the large number of varieties derived from spontaneous mutations that are commercialized in citrus. To identify key traits elicited by citrus domestication, we analyzed transcriptomes from developing fruit pulp of wild inedible Ichang papeda, Sun Chu Sha Kat sour mandarin and three palatable segregants derived from a cross between commercial mandarins. Based on these results, we propose that during the transition from inedible papedas to sour mandarins, domestication involved a first phase of major changes in the expression of genes regulating central pathways of primary and secondary metabolism. This stage was mainly characterized by both the stimulation of growth processes and the reduction of distasteful chemicals defenses. It is also suggested that in a second phase, edible attributes of mandarins, especially acidity, were progressively improved through specific modifications. Other relevant changes included upregulation of genes involved in the synthesis of key substances of pleasant aroma and flavor, and the modulation of sugar transporters. Thus, the transition from inedible papeda to sour mandarin was essentially defined by a drastic reprogramming of gene expression of fundamental metabolic pathways, while modern mandarins evolved later through progressive refinement of palatability properties. Taken together, these observations suggest that the rates of mutations occurring in citrus somatic tissues are consistent with the idea that they have played an important role during the later steps of citrus domestication.