Abstract

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.

Highlights

  • The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species

  • We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication

  • In addition to confirming, using the whole-genome sequence, the parentage of Wilking (King–Willowleaf), Kiyomi (Satsuma–sweet orange) and Fallglo, we find parent– child relationships between two pairs of mandarins (Ponkan is a parent of Dancy; Huanglingmiao is a parent of Satsuma)[34], in addition to the previously established parent–child pair of Willowleaf and Clementine mandarins[2]

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Summary

Conclusion

On the basis of genomic, phylogenetic and biogeographic analyses of 60 diverse citrus and related accessions, we propose that the centre of origin of citrus species was the southeast foothills of the Himalayas, in a region that includes the eastern area of Assam, northern Myanmar and western Yunnan. By distinguishing between pure species, hybrids and admixtures, we could trace the genealogy and genetic origin of the major citrus commercial cultivars. Both the extensive relatedness network among mandarins and sweet orange, and the association of pummelo admixture with desirable fruit traits suggest a complex domestication process. This work presents insights into the origin, evolution and domestication of citrus, and the genealogy of the most important wild and cultivated varieties. A. et al Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. E. et al Citrus phylogeny and genetic origin of important species as investigated by molecular markers. L. The possible role of Yunnan, China, in the origin of contemporary citrus species (Rutaceae).

Methods
Data exclusions
Statistical parameters
Antibodies

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