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Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers

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Abstract

Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity (He) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora, with Fst values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the Fst value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise (Fst) index and Nei’s standard genetic distance tests. The Fst outlier test for deviation from expected distribution between Fst and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.

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Funding

This project was supported by funds received from Hainan Provincial Natural Science Foundation of China (No.2018CXTD342), Overseas Construction Plan for Science and Education Base, China-Africa Center for Research and Education, Chinese Academy of Sciences (Grant No. SAJC201327), and Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (No.1630142018001).

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Author notes

  1. Lin Yan and Collins Ogutu contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops of the Ministry of Agriculture of China, Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China

    Lin Yan, Lifang Huang, Xiaoyang Wang, Yuzhou Long & Yunping Dong

  2. CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China

    Collins Ogutu & Yuepeng Han

  3. University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China

    Collins Ogutu

  4. Dehong Tropical Agriculture Institute of Yunnan, Ruili, 678600, Yunnan, China

    Hua Zhou

  5. Tropical and Subtropical Economic Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, 678025, Yunnan, China

    Yulan Lv

  6. Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China

    Yuepeng Han

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  1. Lin Yan
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Correspondence to Yunping Dong or Yuepeng Han.

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Primer sequences of the ISSR markers are provided in Table 1.

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Yan, L., Ogutu, C., Huang, L. et al. Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers. Plant Mol Biol Rep 37, 204–213 (2019). https://doi.org/10.1007/s11105-019-01148-3

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