Genomic origin of Citrus reticulata “Unshiu”

Abstract

Satsuma mandarin (Citrus reticulata “Unshiu”) is a global cultivar with superior fruit characteristics and ranking among the top citrus cultivars in terms of production. It is also a key contributor to citrus breeding. However, the lack of high-quality genome makes the origin of Satsuma mandarin has long been a matter of debate. Here, we assembled a gap-free, high-quality genome of Satsuma mandarin. Meanwhile, we collected and sequenced 15 indigenous citrus varieties in Zhejiang Province, 12 Satsuma mandarins, 21 citrus hybrids related to Satsuma mandarin, 10 modern citrus varieties, and 7 other mandarins. Through high-resolution genome analysis, we inferred that Satsuma mandarin originated from a cross between C. reticulata “Ruju” ×  C. reticulata “Bendiguang” and proposed that Satsuma mandarin most probably originated in East area in Zhejiang Province of China, where the two parents-like cultivars are still found in a sympatric region to date. These results provide new insights into the origin model of Satsuma mandarin. The spread of mandarin is also discussed, which probably associated with the culture exchange and trade activities between Japan and China from Tang Dynasty and afterwards.

Acknowledgments

We are grateful to Zhenpeng Nie and Xiu Huang of Citrus Research Institute of Zhejiang Province for provide assistance with samples collection. We are grateful to Shiliang Mao, Jiancan Zhou and Jianhua Chen for providing us historical records of Satsuma mandarin. This project was supported by the National Natural Science Foundation of China to Q.X. (no. 31925034), Key S&T Projects of Huangyan to Q.X. (JBGS2022-HYNY03), Key Project of Hubei Provincial Natural Science Foundation to Q.X. (no. 2021CFA017), the Fundamental Research Funds for the Central Universities (2662023PY003).

Author Contributions

Q.X. conceived and designed the project and the strategy. S.L. performed the genomic and origin analysis. S.L. also performed the genome assembly and annotation with the help of Y.H. and L.S. L.W., G.L., F.K., L.S., and H.Y. collected the samples. X.Z. and L.W. identified the fruit phenotype. J.X. provided the historical records of Satsuma mandarin. Q.X. and G.L. coordinated the project with help from X.D., J.X., and F.K. S.L. and Q.X. wrote the manuscript with contributions from X.W. and Y.X.

Data availability statement

Genome assemblies have been deposited in the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession number GWHERCA00000000 (C. reticulata “Unshiu”). The raw data for the assembly have been deposited in the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession PRJCA022822 and in NCBI under accession PRJNA1064391. The detailed accession numbers for the 65 whole-genome sequencing data are listed in Supplementary Table 6. The assembled genome and annotation are also available at http://citrus.hzau.edu.cn/.

Conflict of interests

The authors declare no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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