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 language | English (US) |
|---|---|
| Pages (from-to) | 1653-1669 |
| Number of pages | 17 |
| Journal | Genetic Resources and Crop Evolution |
| Volume | 66 |
| Issue number | 8 |
| DOIs | |
| State | Published - Dec 1 2019 |
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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 journal › Article
}
TY - JOUR
T1 - Analysis of genetic diversity of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites
AU - Tran, Hoa
AU - Kanzaki, Shinya
AU - Triest, Ludwig
AU - Hormaza, Inaki
AU - Kuk, Na Jong
AU - Ming, Ray
AU - Bousquet, Jean
AU - Khasa, Damase
AU - Van Damme, Patrick
PY - 2019/12/1
Y1 - 2019/12/1
N2 - 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.
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.
KW - Conservation and breeding
KW - Fingerprinting
KW - Germplasm
KW - SSR polymorphism
KW - UPGMA
KW - Xerospermum noronhianum
UR - http://www.scopus.com/inward/record.url?scp=85073944988&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85073944988&partnerID=8YFLogxK
U2 - 10.1007/s10722-019-00837-y
DO - 10.1007/s10722-019-00837-y
M3 - Article
AN - SCOPUS:85073944988
VL - 66
SP - 1653
EP - 1669
JO - Genetic Resources and Crop Evolution
JF - Genetic Resources and Crop Evolution
SN - 0925-9864
IS - 8
ER -