Abstract
We report 12 microsatellites enriched in CT repeats obtained from a genomic library of the lychee (Litchi chinensis Sonn.) cultivar Mauritius. The polymorphisms revealed by these microsatellites were evaluated in a collection of 21 lychee cultivars. A total of 59 fragments were detected with these 12 SSRs, with an average of 4.9 bands/SSR. Three primer pairs seem to amplify more than a single locus. The mean expected and observed heterozygosities over the 9 single-locus SSRs averaged 0.571 (range: 0.137–0.864) and 0.558 (range: 0.169–0.779) respectively. The total value for the probability of identity was 7.53×10-5. In addition, the selected SSRs were used to amplify DNA from four longan cultivars. Eleven of the 12 SSRs produced amplification fragments in longan, and eight of these fragments were polymorphic. All except two of the products amplified from longan were the same size as those amplified from lychee, suggesting a close genetic proximity between the two species. The SSRs studied produced 22 different patterns, allowing the unambiguous identification of 16 lychee and the 4 longan cultivars studied. Discrimination was possible with just four selected microsatellites. Two groups with two and three undistinguishable cultivars were obtained, reflecting probable synonymies. Unweighted pair-group method of artimetic averages (UPGMA) cluster analysis divided the lychee cultivars studied into two main groups, one consisting of ancient cultivars and the other with more diverse recent cultivars. This is the first report of microsatellite development in the Sapindaceae, and the results demonstrate the usefulness of microsatellites for identification, similarity studies and germplasm conservation in lychee and related species.
Similar content being viewed by others
References
Anuntalabhochai R, Chundet R, Chiangda J, Apavatjrut P (2002). Genetic diversity within lychee (Litchi chinensis Sonn.) based on RAPD analysis. Acta Hortic 575:253–259
Aradhya MK, Zee FT, Manshardt RM (1995) Isozyme variation in lychee (Litchi chinensis Sonn.). Sci Hortic 63:21–35
Billote N, Lagoda PJL, Risterucci A-M, Baurens F-C (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288
Degani C, Beiles A, El-Batsri R, Goren M, Gazit S (1995a) Identifying lychee cultivars by isozyme analysis. J Am Soc Hortic Sci 120:307–312
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 120:523–526
Ellegren H, Primmer CR, Sheldon BC (1995). Microsatellite evolution, directionality or bias. Nat Genet 11:360–362
Fulton TM., Chunwongse J, Tanksley SD (1995). Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Rep 13:207–209
Galán-Saúco V, Fernández-Galván D, Hernández-Delgado PM (2001) Behavior of different litchi cultivars in the Canary Islands. Acta Hortic 558:83–88.
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis in bread wheat. Euphytica 113:163–185
Hamilton MB, Pincus EL, Di Fiore A, Fleischer RC (1999) Universal linkers and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:500–507
Hormaza JI (2002) Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theor Appl Genet 104:321–328
Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401
McConchie CA, Vithanage V, Batten DJ (1994) Intergeneric hybridisation between litchi (Litchi chinensis Sonn.) and longan (Dimocarpus longan Lour.). Ann Bot 74:111–118
Menzel C (2002). The lychee crop in Asia and the Pacific. FAO, Bangkok
Menzel CM, Simpson DR (1986) Lychee cultivars - description and performance of major lychee cultivars in subtropical Queensland. Qld Agric J 112:125–136
Menzel CM, Simpson DR (1990) Performance and improvement of lychee cultivars: a review. Fruit Varieties J 44:197–215
Menzel CM, Simpson DR (1991) A description of lychee cultivars. Fruit Var J 45:45–56
Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 93:1282–1290
Morton J (1987) Fruits of warm climates. Miami, Florida
Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273
Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354
Perry DJ, Bousquet J (1998) Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theor Appl Genet 97:735–743
Steinkellner H, Lexer C, Turetschek E, Glossl J (1997) Conservation of (GA)n microsatellite loci between Quercus species. Mol Ecol 6:1189–1194
Stern RA, Gazit S (1996) Lychee pollination by the honeybee. J Am Soc Hortic Sci 120:152–157
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
Van de Wiel C, Arens P, Vosman B (1999) Microsatellite retrieval in lettuce (Lactuca sativa L.). Genome 42:139–149
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 18:5–16
Watson BJ, Menzel CM, Jordan AT (1988) Lychees - cultivar names. Farm Note Qld Dept Prim Indust F44
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, NY, pp 159–181
Weber J, May P (1989) Abundant class of humans DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Wright S (1951) The genetic structure of populations. Ann Eugen 15:323–354
Wünsch A, Hormaza JI (2002) Cultivar identification and genetic fingerprinting of temperate fruit tree species using DNA markers. Euphytica 125:59–67
Zane L, Bargelloni L, and Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Acknowledgements
We gratefully acknowledge J.M. Hermoso for valuable information on lychee germplasm. Financial support for this work was provided by MCYT (Project Grant AGL2001-2414-C04-03)
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by H.F. Linskens
Rights and permissions
About this article
Cite this article
Viruel, M.A., Hormaza, J.I. Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae). Theor Appl Genet 108, 896–902 (2004). https://doi.org/10.1007/s00122-003-1497-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-003-1497-4