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United States Department of Agriculture

Agricultural Research Service

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Nut Research

Title: Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

item Rokhsar, Daniel -
item Chen, Chunxian
item Wu, Albert -
item Prochnik, Simon -
item Jenkins, Jerry -
item Salse, Jerome -
item Hellsten, Uffe -
item Murat, Florent -
item Perrier, Xavier -
item Ruiz, Manuel -
item Scalabrin, Simone -
item Terol, Javier -
item Takita, Marco -

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 4, 2014
Publication Date: June 8, 2014
Citation: Rokhsar, D., Chen, C., Wu, A.G., Prochnik, S., Jenkins, J., Salse, J., Hellsten, U., Murat, F., Perrier, X., Ruiz, M., Scalabrin, S., Terol, J., Takita, M.A. 2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology.

Interpretive Summary: Diverse types of commercial citrus cultivars were domesticated several thousand years ago in Southeast Asia and spread globally. According to limited morphologic traits and molecular marker data, most citrus types are presumably originated from interspecific hybridization and multi-generational introgression with different wild ancestral species. However, it remains controversial how main modern varieties evolved from what ancestral species. This study is to sequence and compare the genomes of main citrus types, including mandarins, pummelos, sweet oranges and sour oranges. The results help understand taxonomic relationship from genomic phylogenetic perspectives and facilitate sequence-directed genetic improvement in the crop.

Technical Abstract: Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild ‘mandarin’ diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.

Last Modified: 7/28/2015
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