Genome of wild mandarin and domestication history of mandarin

Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to occur in South China, which has been one of the cultivation centers for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. The citric acid level was dramatically reduced in cultivated mandarins. To understand the genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. The results showed that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South of the Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group, there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a genomic region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.