Genetic Resources and Crop Evolution

, Volume 65, Issue 3, pp 1035–1048 | Cite as

Genetic diversity and differentiation of the Hainan Tall coconut (Cocos nucifera L.) as revealed by inter-simple sequence repeat markers

  • Kun Pan
  • Wenquan Wang
  • Haiyan Wang
  • Haikuo Fan
  • Yi Wu
  • Longxiang Tang
Research Article


Hainan Tall coconut (Cocos nucifera L.), which show the advantageous characteristics of high yield, hardiness, and wind resistance, is the dominant coconut population in Hainan Island, the main area of coconut production in China. An understanding of the genetic diversities and origins of the Hainan Tall population is essential to effective breeding. To achieve this aim, we used dozens of inter-simple sequence repeat molecular markers to characterize the genetic diversity among Hainan Tall and other coconut accessions outside China. Results revealed that Hainan Tall consisted of two main subgroups reflecting different geographic distributions (such as northern vs. southern parts of Hainan Island), and other accessions lacking clear location trends because of human activities. Diversity analysis revealed that the Hainan Tall population exhibits a higher genetic diversity than that of exotic populations mostly collected from Southeast Asia. The phylogenetic clustering results indicated that the Hainan Tall population is domesticated separately from (and earlier than) other coconut accessions, and the differentiation existed within the Hainan Tall population. Among other causes, this notion may explain the high diversity within the Hainan Tall population. Overall, these findings provide a preliminary scenario of the genetic diversities and origins of the Hainan Tall population.


Cocos nucifera Genetic diversity Differentiation Origin 



Amplified fragment length polymorphisms


Inter-simple sequence repeats


Neighbor joining


Principal coordinate analysis


Restriction fragment length polymorphisms


Randomly amplified polymorphic DNA


Simple sequence repeats


Sequential hierarchical and nested clustering


Unweighted pair group method with arithmetic averages



The authors thank the donors of the coconut accessions from outside Hainan and the Coconut Institute of the CATAS. They also thank all participants in the investigation into the native coconut germplasm and the collection of samples of the Hainan Tall accessions. Finally, they are grateful to Dr. Guanping Yang for revising the manuscript.


This study was funded by a joint collaborative project of the Institute of Tropical Biosciences & Biotechnology (ITBB) with the CRI of the CATAS and Special Foundation for Scientific Research on (Agricultural) Industry (Grant No. 200903026).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Data Archiving Statement

We used the universal ISSR primers described by the University of British Columbia, Canada (Michael Smith Laboratories, University of British Columbia, Primer set #9, Vancouver, BC, Canada) and hold no other data obtained from or submitted to any other public database.


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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  1. 1.Coconut Research InstituteChinese Academy of Tropical Agriculture SciencesWenchangPeople’s Republic of China
  2. 2.Institute of Tropical Biosciences and BiotechnologyChinese Academy of Tropical Agriculture SciencesHaikouPeople’s Republic of China
  3. 3.Hainan Medical UniversityHaikouPeople’s Republic of China

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