NEW INSIGHTS INTO THE PHYLOGENY AND SPECIATION OF KUMQUAT (FORTUNELLA SPP.) BASED ON CHLOROPLAST SNP, NUCLEAR SSR AND WHOLE-GENOME SEQUENCING

Highlights

● Fortunella genus consists of two populations: cultivated kumquat and wild Hong Kong kumquat.

● Artificial selection might involve in the origin of cultivated Fortunella species.

● A hypothesis for the differentiation and speciation of Fortunella species is proposed.

Abstract

Kumquat (Fortunella spp.) is a fruit and ornamental crop worldwide due to the palatable taste and high ornamental value of its fruit. Although Fortunella is classified into the economically important true citrus fruit tree group together with Citrus and Poncirus, few studies have been focused on its evolutionary scenario. In this study, analysis of five chloroplast loci and 47 nuclear microsatellites (nSSR) loci from 38 kumquat and 10 citrus accessions revealed the independent phylogeny of Fortunella among citrus taxa, and that Fortunella mainly comprises two populations: CUL, cultivated Fortunella spp. (F. margarita, F. crassifolia and F. japonica); and HK, wild Hong Kong kumquat (Fortunella hindsii). Genomic analysis based on whole-genome SNPs indicated that the allele frequency of both pupations deviated from the neutral selection model, suggesting directional selection was a force driving their evolutions. CUL exhibited lower genomic diversity and higher linkage strength than HK, suggesting artificial selection involved in its origin. A high level of genetic differentiation (Fst = 0.364) was detected and obviously asynchronous demographic changes were observed between CUL and HK. Based on these results, a new hypothesis for the speciation of Fortunella is proposed.

Graphical abstract

Keywords

Citrus / Fortunella / kumquat / phylogenetics

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Supplementary materials

The online version of this article at https://doi.org/10.15302/J-FASE-2021436 contains supplementary materials (Figs. S1–S5; Tables S1–S11; supplementary data set). Resequencing data are available in the CNCB-NGDC database (BioProject PRJCA005010) and NCBI database (BioProject PRJNA736109).

Acknowledgements

This work was funded by the National Key Research and Development Program of China (2018YFD1000106), the National Natural Science Foundation of China (31630065), and Special Project for External Science and Technology Cooperation of Science and Technology Department of Yunnan Province (202003AD150014). We sincerely thank Prof. Jian Li (Department of Agriculture of Fujian Province, China), Prof. Jian’guo Xu (Citrus Research Institute of Zhejiang Province, China), Prof. Shiping Zhu (Citrus Research Institute of CAAS, China), Prof. Wu Wen (Guangdong Academy of Agricultural Sciences, China), Zhenhua Tan (Agricultural Bureau of Yizhang, China), Prof. Guohua Li (Meizhou Academy of Agricultural Sciences, China), and Prof. Min Zhang (Zhejiang A&F University, China) for their assistance in sample collection.

Compliance with ethics guidelines

Chenqiao Zhu, Peng Chen, Junli Ye, Hang Li, Yue Huang, Xiaoming Yang, Chuanwu Chen, Chenglei Zhang, Yuantao Xu, Xiaoli Wang, Xiang Yan, Guangzhou Deng, Xiaolin Jiang, Nan Wang, Hongxing Wang, Quan Sun, Yun Liu, Di Feng, Min Yu, Xietian Song, Zongzhou Xie, Yunliu Zeng, Lijun Chai, Qiang Xu, Chongling Deng, Yunjiang Cheng, and Xiuxin Deng declare that they have no conflicts of interest or financial conflicts to disclose. This article does not contain any study with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

The Author(s) 2022. Published by Higher Education Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0)