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

Hoa Tran, Shinya Kanzaki, Ludwig Triest, Inaki Hormaza, Na Jong Kuk, Ray Ming, Jean Bousquet, Damase Khasa, Patrick Van Damme

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1653-1669
Number of pages17
JournalGenetic Resources and Crop Evolution
Volume66
Issue number8
DOIs
StatePublished - Dec 1 2019

Fingerprint

Sapindaceae
Litchi
Litchi chinensis
Vietnam
Microsatellite Repeats
cultivar
microsatellite repeats
genetic variation
cultivars
litchis
domestication
genomic libraries
germplasm
germplasm conservation
subpopulation
villages
genomics
polymorphism
village
genetic polymorphism

Keywords

  • Conservation and breeding
  • Fingerprinting
  • Germplasm
  • SSR polymorphism
  • UPGMA
  • Xerospermum noronhianum

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

Analysis of genetic diversity of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites. / Tran, Hoa; Kanzaki, Shinya; Triest, Ludwig; Hormaza, Inaki; Kuk, Na Jong; Ming, Ray; Bousquet, Jean; Khasa, Damase; Van Damme, Patrick.

In: Genetic Resources and Crop Evolution, Vol. 66, No. 8, 01.12.2019, p. 1653-1669.

Research output: Contribution to journalArticle

Tran, Hoa ; Kanzaki, Shinya ; Triest, Ludwig ; Hormaza, Inaki ; Kuk, Na Jong ; Ming, Ray ; Bousquet, Jean ; Khasa, Damase ; Van Damme, Patrick. / Analysis of genetic diversity of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites. In: Genetic Resources and Crop Evolution. 2019 ; Vol. 66, No. 8. pp. 1653-1669.
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AU - Hormaza, Inaki

AU - Kuk, Na Jong

AU - Ming, Ray

AU - Bousquet, Jean

AU - Khasa, Damase

AU - Van Damme, Patrick

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AB - 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.

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