Genome of Wild Mandarin and Domestication History of Mandarin

Abstract

Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found 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 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 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.

Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

“…3B), indicating its potential association with callus initiation, because empirically, EC can only be induced from the seeds of the polyembryonic citrus genotypes. With the availability of the citrus genome sequences [43][44][45][46][47], two orthologs of CsARF19, MSYJ162170.1 (amino acids sequence identity of 99.36%) and…”

“…Ciclev10030751m (amino acids sequence identity of 99.87%), were identified in Mangshan mandarin (Citrus reticulate, a wild mandarin) and Clementine mandarin (C. clementina which is believed to be a chance hybrid of mandarin and sweet orange) [45,47,48], respectively, but not in atalantia…”

“…Finally, a self-blast of these protein sequences was performed to remove the redundancy whereas the alternative splice variants were not considered. A total of seven draft genomes of citrus species, including Mangshan mandarin, Clementine mandarin, atalantia, Ichang papeda, kumquat, trifoliate orange (unpublished data) and citron, were used to search the orthologs of CsARF19 [44][45][46][47].…”

CitGVD: a comprehensive database of citrus genomic variations

“…The worldwide production and total acreage of citrus fruits ranks first among all fruit crops. The most widely cultivated citrus species under domestication and selective breeding include sweet orange (Citrus sinensis), mandarin (Citrus reticulata), pummelo (Citrus grandis), grapefruit (Citrus paradisi), and lemon (Citrus limon) 1,2 . Draft genome sequences of several citrus species have been released in genomic databases citrus annotation project (CAP) 3 and Phytozome 4,5 .…”

Putative Synergetic Genes Involved in the Syntheses of Carotenoids and Flavonoids in 'Cara cara' Navel Orange as Revealed by Integrated Transcriptome and Metabolomics Analysis

“…Citrus is one of the most important fruits in the world, and is rich in various primary and secondary metabolites, such as amino acids, organic acids, soluble sugars, avonoids, volatile terpenoids, limonoids, coumarins and carotenoids [1][2][3][4][5]. Some metabolites, including avonoids, limonoids, organic acids and soluble sugars, were reported to contribute to fruit taste [3,4], whilst terpenoids and carotenoids were associated with fruit aroma and color [2,6].…”