Advertisement

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
  • 48 Downloads

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.

Keywords

Xerospermum noronhianum SSR polymorphism Fingerprinting UPGMA Germplasm Conservation and breeding 

Notes

Acknowledgements

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.

Funding

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)

References

  1. Anuntalabhochai R, Chundet R, Chiangda J, Apavatjrut P (2002) Genetic diversity within lychee (Litchi chinensis Sonn.) based on RAPD analysis. Acta Hortic 575:253–259CrossRefGoogle Scholar
  2. Aradhya MK, Zee FT, Manshardt RM (1995) Isozyme variation in lychee (Litchi chinensis Sonn.). Sci Hortic 63:21–35CrossRefGoogle Scholar
  3. Baoyao W et al (2011) Chemical compositional characterization of ten litchi cultivars. IEEE. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5943958. Accessed 2015
  4. Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, Plomion C, Villani F, Kremer A (2004) Comparative mapping between Quercus and Castanea using simplesequence repeats (SSRs). Theor Appl Genet 108:558–566CrossRefGoogle Scholar
  5. Chybicki IJ, Burczyk J (2013) Seeing the forest through the trees: comprehensive inference on individual mating patterns in a mixed stand of Quercus robur and Q. petraea. Ann Bot 112(3):561–574.  https://doi.org/10.1093/aob/mct131 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Degani C, Beiles A, El-Batsri R, Goren M, Gazit S (1995a) Identifying lychee cultivars by isozyme analysis. J Am Soc Hortic Sci 120:307–312CrossRefGoogle Scholar
  7. Degani C, Stern RA, El-Batsri R, Gazit S (1995b) Pollen parent effect on the selective abscission of ‘Mauritius’ and ‘Floridian’ lychee fruitlets. J Am Soc Hortic Sci 120:523–526CrossRefGoogle Scholar
  8. Ekué et al (2009) Transferability of simple sequence repeat (SSR) markers developed in Litchi chinensis to Blighia sapida (Sapindaceae). Plant Mol Biol Rep 27(4):570–574CrossRefGoogle Scholar
  9. FVRI Annual Report (2009) Fruit and Vegetable Research Institute, pp 209–213 (Unpublished)Google Scholar
  10. FVRI Annual Report (2015) Fruit and Vegetable Research Institute (FVRI) Annual Report (Unpublished)Google Scholar
  11. Glenn TC, Schable NA (2005) Isolating microsatellite DNA loci. Methods Enzymol 395:202–222CrossRefGoogle Scholar
  12. Goldstein D, Schlötterer C (1999) Microsatellites: evolution and applications. Oxford University Press, OxfordGoogle Scholar
  13. Goudet J (2002) Fstat Vision (1.2): a computer program to calculate F-statistics. J Hered 86:485–486CrossRefGoogle Scholar
  14. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2(4):618–620.  https://doi.org/10.1046/j.1471-8286.2002.00305.x CrossRefGoogle Scholar
  15. Kibbe WA (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35(webserver issue):43–46CrossRefGoogle Scholar
  16. Kim et al (2010) Pollinators of Micromelum minutum in Vietnam. MS thesis, University of Århus, Department of Genetics and Ecology, Ny Munkegade Block 540, DK-8000 Aarhus C, DenmarkGoogle Scholar
  17. Lee YQ (1989) ‘Hemaoli’ (Litchi chinensis var. fulvosus Lee): a new varieties of lychee. Commun Litchi Technol 1:21–22Google Scholar
  18. Leenhouts PW (1978) Systematic notes on the Sapindaceae-Nephelieae. Blumea 24:395–403Google Scholar
  19. Li MF, Zheng XQ (2004) Development of SSR markers in lychee (Litchi chinensis). Yi Chuan 26(6):911–916 (in Chinese) PubMedGoogle Scholar
  20. Li M et al (2006) Development and characterization of SSR markers in lychee (Litchi chinensis). Mol Ecol Notes 6:1205–1207.  https://doi.org/10.1111/j.1471-8286.2006.01492el CrossRefGoogle Scholar
  21. Liu CM, Mei MT (2002) Researches on DNA isolation and optimal parameters of RAPD in some Sapindaceae fruit trees. Adv Hortic Guangzhou Publ 5:297–302 (in Chinese) Google Scholar
  22. Liu CM, Mei MT (2003) Classification of litchi (Litchi chinensis Sonn.) cultivars based on RAPD analysis. Acta Hortic 625:131–136Google Scholar
  23. Liu W et al (2015) Identifying litchi (Litchi chinensis Sonn) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers. PLoS ONE.  https://doi.org/10.1371/journal.pone.0135390 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Madhou M, Bahorun T, Hormaza JI (2010) Phenotypic and molecular diversity of litchi cultivars in Mauritius. Fruits 65:141–152CrossRefGoogle Scholar
  25. Madhou M, Normand F, Bahorun T, Hormaza JI (2012) Fingerprinting and analysis of genetic diversity of litchi (Litchi chinensis Sonn.) accessions from different germplasm collections using microsatellite markers. Tree Genet Genomes.  https://doi.org/10.1007/s11295-012-0560-1 CrossRefGoogle Scholar
  26. MARD (2003–2007, 2016) Annual reports from Department of Agriculture and Rural Development, DARDs for the period of 2003–2007, pp 456–543Google Scholar
  27. Matsumoto Brower TK (2006) Genes uniquely expressed in vegetative and potassium chlorate induced floral buds of dimocarpus longan. Plant Sci 170:500–516CrossRefGoogle Scholar
  28. McConchie CA, Vithanage V, Batten DJ (1994) Intergeneric hybridisation between litchi (Litchi chinensis Sonn.) and longan (Dimocarpus longan Lour.). Ann Bot 74:111–118CrossRefGoogle Scholar
  29. Menzel CM, Simpson DR (1990) Performance and improvement of lychee cultivars: a review. Fruit Var J 44:197–215Google Scholar
  30. Menzel CM, Simpson DR (1991) A description of lychee cultivars. Fruit Var J 45:45–56Google Scholar
  31. Michalakis Y, Excoffier L (1996) A generic estimation of population subdivision using distances between alleles with special interest to microsatellite loci. Genetics 142:1061–1064PubMedPubMedCentralGoogle Scholar
  32. Nguyen TB (2000) Vietnam Academy of Science and Technology, Institute of Ecology and Biological Resources (VAST, IEBR). Annual Report, pp 65–76Google Scholar
  33. Nguyen (2003) Forest Institute of Plant Investment (FIPI). Annual Report, pp 109–115Google Scholar
  34. Nguyen VZD et al (2003) Forest Institute of Plant Investment (FIPI). Annual Report, pp 109–115Google Scholar
  35. Nguyen et al (2008–2009) In: Institute of agricultural genetics. Annual report, pp 201–214 (Unpublished, in Vietnamese)Google Scholar
  36. Österberg MK, Shavorskaya O, Lascoux M, Lagercrantz U (2002) Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time. Genetics 161(1):299–306PubMedPubMedCentralGoogle Scholar
  37. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes.  https://doi.org/10.1111/j.1471-8286.2005.01155.x CrossRefGoogle Scholar
  38. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287CrossRefGoogle Scholar
  39. Pritchard JK, Stephens M, Donnelly P et al (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  40. Ramanatha Rao V et al (2005) Lychee genetic resources conservation and utilization in Asia—IPGRI’s efforts. Acta Hortic 665:117–224Google Scholar
  41. Rossetto M (2001) Sourcing of SSR markers from related plant species. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CAB International, Oxford, pp 210–224Google Scholar
  42. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  43. Schroeder JW, Tran HT, Dick CW (2014) Fine scale spatial genetic structure in Pouteria reticulata (Engl) Eyma (Sapotaceae), a dioecious, vertebrate dispersed tropical rain forest tree species. Glob Ecol Conserv 1:43–49CrossRefGoogle Scholar
  44. Sim CH, Mahani MC, Choong CY, Salma I (2005) Transferability of SSR markers from lychee (Litchi chinensis Sonn.)to pulasan (Nephelium ramboutan-ake L.). Fruits 60:379–385CrossRefGoogle Scholar
  45. Slotte T, Huang H, Holm K, Ceplitis A, St. Onge K, Chen J, Lagercrantz U, Lascoux M (2009) Splicing variation at a FLOWERING LOCUS C homoeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris. Genetics.  https://doi.org/10.1534/genetics.109.103705 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Tan PJ (2008) Phytochemical characterization of Xerospermum Noronhianum. PhD thesis, Universiti Putra MalaysiaGoogle Scholar
  47. Tan PJ, Khozirah S, Christian P, Intan SI, Faridah A, Nordin HL, Viqar UA (2009) Bidesmosidic Oleanane Saponins from Xerospermum noronhianum. Helv Chim Acta 92:1973–1982CrossRefGoogle Scholar
  48. Taylor JS, Durkin JMH, Breden F (1999) The death of a microsatellite: a phylogenetic perspective on microsatellite interruptions. Mol Biol Evol 16:567–572CrossRefGoogle Scholar
  49. Tran HT (2003) Agrobiodiversity Project (VIE/01/G35) proceedings, pp 112–119 (UNDP Library)Google Scholar
  50. Tran HT et al (2000) Agrobiodiversity Project (VIE/01/G35) Annual Report (UNDP Library)Google Scholar
  51. Tran et al (2017) Utilization and conservation of an indigenous-underutilized fruit tree species: Xerospermum noronhianum (Sapindaceae). In: European conference of tropical ecology, Brussels, Belgium (Abstract Book)Google Scholar
  52. Tran HT et al (2005) In situ conservation of native lychee and their wild relatives and participatory market analysis and development—the case of Vietnam. Acta Hortic 665:125–140Google Scholar
  53. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4(3):535–538CrossRefGoogle Scholar
  54. Varshney RK, Kumar A, Balyan HS, Roy JK, Prasad M, Gupta PK (2000) Characterization of microsatellites and development of chromosome specific STMS markers in bread wheat. Plant Mol Biol Rep 18:5–16CrossRefGoogle Scholar
  55. Viruel MA, Hormaza JI (2004) Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae). Theor Appl Genet 108:896–902.  https://doi.org/10.1007/s00122-003-1497-4 CrossRefPubMedGoogle Scholar
  56. Weber JL (1990) Human DNA polymorphisms based on length variations in simple-sequence tandem repeats. In: Davis KE, Tilghman SM (eds) Genome analysis, vol 1. Genetic and physical mapping. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 159–181Google Scholar
  57. Wright S (1951) The genetic structure of populations. Ann Eugen 15:323–354CrossRefGoogle Scholar
  58. Yap I, Nelson RJ (1996) Winboot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI. Discussion Paper Series no. 14, International Rice Institute, Manila, PhilippinesGoogle Scholar

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

Personalised recommendations