Citrus fruits are globally significant crops, and China is recognized as an important center of mandarin domestication. The Satsuma mandarin has played a key role in citrus cultivation and breeding due to its excellent quality and stress tolerance, leading to widespread commercial production worldwide. However, historical records and genetic evidence regarding its geographic and parental origin have remained inconclusive. Earlier hypotheses alternately proposed China or Japan as the birthplace, and prior molecular analyses lacked resolution to confirm its parental lineage. These uncertainties have hindered both accurate documentation of citrus domestication and efforts to innovate breeding strategies. Based on these challenges, it is necessary to conduct deeper research on the genetic origin of Satsuma mandarin.
Researchers from Huazhong Agricultural University and collaborating institutions published a study (DOI: 10.1093/hr/uhaf015) on May 1, 2025, in Horticulture Research, providing the first gap-free reference genome of Satsuma mandarin. Through high-depth sequencing of 65 citrus accessions and comparative genomic analyses, the team identified that Satsuma mandarin most likely originated in Zhejiang Province, China, through a natural hybridization event between the “Ruju” mandarin as the seed parent and the “Bendiguang” mandarin as the pollen parent.
The study assembled a high-quality, telomere-to-telomere (T2T) diploid genome for Satsuma mandarin, significantly improving completeness and continuity over previous versions. Researchers then sequenced and analyzed 65 citrus varieties, including indigenous mandarins from Zhejiang, modern cultivars, and known hybrids. Genomic landscape comparisons and identity-by-descent analyses showed that Satsuma mandarin shares a nearly identical genomic structure with native cultivars from Zhejiang. Statistical modeling revealed a 96.6% probability that Satsuma mandarin originated from a cross between the “Ruju” mandarin and “Bendiguang” mandarin. The study further linked key flavor and seedlessness traits to specific genomic regions, including transporter and male-sterility–related genes. Historical analysis also supported the hypothesis that citrus fruits spread from eastern China to Japan during cultural exchange periods such as the Tang and Song dynasties. Together, these findings present the most conclusive evidence to date regarding the biological and geographic origin of Satsuma mandarin, while providing improved genomic resources for breeding programs.
“This research not only resolves a long-standing debate in citrus evolutionary history but also offers practical value for future mandarin breeding,” said the study's corresponding author. “By clarifying the ancestry and genetic structure of Satsuma mandarin, we can now design informed hybridization strategies to break its narrow genetic background and develop new cultivars with improved fruit quality and climate resilience.”
The clarified origin and newly established genome provide valuable guidance for breeding seedless, stress-resilient, and high-flavor mandarin varieties. The ability to identify parental lines and recombination patterns enables breeders to expand genetic diversity, overcoming the limitations imposed by Satsuma mandarin’s historically narrow lineage. In addition, the study highlights eastern China as an important reservoir of citrus genetic resources, supporting conservation programs for indigenous cultivars. More broadly, the findings showcase how genomics can connect agricultural practices with cultural and historical pathways of crop domestication.
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References
DOI
10.1093/hr/uhaf015
Original Source URL
https://doi.org/10.1093/hr/uhaf015
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.