Genetic Resources and Crop Evolution

, Volume 66, Issue 8, pp 1653–1669 | Cite as

Analysis of genetic diversity of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites

  • Hoa TranEmail author
  • Shinya Kanzaki
  • Ludwig Triest
  • Inaki Hormaza
  • Na Jong Kuk
  • Ray Ming
  • Jean Bousquet
  • Damase Khasa
  • Patrick Van Damme
Research Article


We report on 14 microsatellites enriched in CT repeats obtained from a genomic library of lychee (Litchi chinensis Sonn.) cultivar “Hong Huay”. The polymorphisms revealed by these microsatellites were evaluated in a collection of 45 local Vietnamese lychee varieties and 4 Xerospermum noronhianum (Blume) Blume (Sapindaceae) collected from the wild. Samples were collected from local villages and forests in northern Vietnam. Genetic diversity parameters were estimated for the local Vietnamese varieties analyzed. The unweighted pair-group method of clustering using averages divided the lychee cultivars into three main groups: Cluster 1 (Group A) consisting of semi-natural lychees (“extremely early” lychee); Cluster 2 (Group B) consisting of cultivated cultivars (“intermediate” lychee); and Cluster 3 (Group C) representing X. noronhianum accessions. Using STRUCTURE, three subpopulations were also delimited among litchi accessions, including accessions with extremely early- and intermediate/late-maturing traits showing membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and intermediate-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. This is the first report on transferability of SSR markers developed from lychee (L. chinensis) to X. noronhianum. Results demonstrate the usefulness of microsatellites for identification, genetic diversity analysis and germplasm conservation in lychee and related Sapindaceae forest species.


Xerospermum noronhianum SSR polymorphism Fingerprinting UPGMA Germplasm Conservation and breeding 



Sincere appreciation is expressed to Dr. Francis Zee (USDA, ARS), for his useful suggestions and correction on scientific name and English name of rambutan and X. noronhianum. This work was supported by Grant-in-Aid (No. 200706) for Scientific Research from the Ministry of Science and Technology from Japan and Vietnam and the Erasmus Mundus-Lotus Projects for South-East Asian from European commission and the host institution, Vrije Universiteit Brussels (VUB). This work was supported partly by the Ray Ming lab at the University of Illinois at Urbana and Champaign (UIUC); the Khasa & Bousquet labs (Canada Research Chair in Forest Genomics, University Laval) on running of additional PCR and litchi SSR analysis (at the Institute of Integrative Biology and System, University Laval). Many thanks to the University Laval team of lab assistants and managers from whom I received their full guidance: M.E. Beaulieu, P. Gagné, S. Senneville, and special thanks to S. Gérardi for his useful comments on the labelled primers.


The authors confirm that there has been no significant financial support for this work that could have influenced its outcome.

Compliance with ethical standards

Conflict of interest

The authors confirm that there are no known conflicts of interest associated with this publication.

Supplementary material

10722_2019_837_MOESM1_ESM.xls (34 kb)
Supplementary material 1 (XLSX 34 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Institute of Agricultural GeneticsHanoiVietnam
  2. 2.Faculty of AgricultureKindai UniversityNaraJapan
  3. 3.Vrije Universiteit BrusselBrusselsBelgium
  4. 4.E.E. la Mayora – CSICAlgarrobo-CostaSpain
  5. 5.Department of Controlled AgricultureKangwon National UniversityChuncheon-siRepublic of Korea
  6. 6.FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignChampaignUSA
  7. 7.Canada Research Chair in Forest Genomics, Forest Research Centre and Institute of Integrative Biology and SystemsUniversité LavalQuebecCanada
  8. 8.Ghent UniversityGhentBelgium
  9. 9.Faculty of Tropical AgriSciencesCzech University of Life Sciences PraguePrague 6-SuchdolCzech Republic

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