Skip to main content Accessibility help

An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers

  • Kouhei Kuwahara (a1), Reimi Suzuki (a1), Yusuke Ito (a1), Tetsuo Mikami (a1) and Yasuyuki Onodera (a1)...


To assess the genetic diversity of spinach germplasm, 250 individuals of 50 accessions collected from geographically diverse regions (West Asia, East Asia, Japan, Europe and the USA) were analysed using simple sequence repeat (SSR) markers. A total of 39 polymorphic alleles were identified, with an average of 6.5 alleles per locus for six loci. The overall gene diversity (0.62) in the entire set of individuals suggests that the germplasm has high genetic variability. The West Asian accessions showed the highest gene diversity, with a value of 0.57, followed by the East Asian accessions. These results help confirm the notion that spinach originated from West Asia. Hierarchical analysis of molecular variance revealed significant genetic differentiation among the geographical regions, which accounts for 26% of the total variation detected. Furthermore, pairwise Φst values indicate low genetic differentiation between the East Asian and Japanese germplasm accessions, both of which showed high genetic differentiation from the European accessions. The differentiation between the East Asian and European gene pools may be attributed to the founder effect associated with crop dissemination, as well as to the selection and genetic drift that occurred during the breeding process.


Corresponding author

* Corresponding author. E-mail:


Hide All
Borner, A, Chebotar, S and Korzun, V (2000) Molecular characterization of the genetic integrity of wheat (Triticum aestivum L.) germplasm after long-term maintenance. Theoretical and Applied Genetics 100: 494497.
Brandenberger, L, Morelock, T and Correll, J (1992) Evaluation of spinach germplasm for resistance to a new race (Race 4) of Peronospora farinosa f. sp. spinaciae. HortScience 27: 11181119.
Cavallis-Sforza, LL and Edwards, AWF (1967) Phylogenetic analysis. Models and estimation procedures. Evolution 21: 550570.
Doyle, JJ and Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12: 1315.
Gao, LZ and Innan, H (2008) Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics 179: 965976.
Groben, R and Wricke, G (1998) Occurrence of microsatellites in spinach sequences from computer databases and development of polymorphic SSR markers. Plant Breeding 117: 271274.
Hammer, K (2001) Chenopodiaceae, Spinacia oleracea L. In: Hanelt, P and Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben Germany (eds) Mansfeld's Encyclopedia of Agricultural and Horticultural Crops (Except Ornamentals), 1st English edn. Berlin: Springer, pp. 249251.
Hu, J, Mou, B and Vick, B (2007) Genetic diversity of 38 spinach (Spinacia oleracea L.) germplasm accessions and 10 commercial hybrids assessed by TRAP markers. Genetic Resources and Crop Evolution 54: 16671674.
Ishiguro, K (1982) Hourenso. In: Sengo-nougyou-hattatsushi 4 Yasai-Kakisaku-Hen (in Japanese) . Tokyo, Japan: The Nippon Agricultural Research Institute, pp. 720736.
Jansen, J, Verbakel, H, Peleman, J and van Hintum, TJ (2006) A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers. Theoretical and Applied Genetics 112: 554561.
Khattak, J, Christiansen, J, Torp, A and Andersen, S (2007) Genic microsatellite markers for discrimination of spinach cultivars. Plant Breeding 126: 454456.
Khattak, J, Torp, A and Andersen, S (2006) A genetic linkage map of Spinacia oleracea and localization of a sex determination locus. Euphytica 148: 311318.
Liu, KJ and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.
Mou, B (2007a) Leafminer-resistant spinach germplasm 03-04-9. HortScience 42: 699700.
Mou, B (2007b) Leafminer-resistant spinach germplasm 03-04-63. HortScience 42: 17171718.
Mou, B (2008a) Evaluation of oxalate concentration in the U.S. spinach germplasm collection. HortScience 43: 16901693.
Mou, B (2008b) Leafminer resistance in spinach. HortScience 43: 17161719.
Nonnecke, IL (1989) Spinach. In: Nonnecke, IL (ed.) Vegetable Production. New York, NY: Van Nostrand Reinhold, pp. 476484.
Parzies, HK, Spoor, W and Ennos, RA (2000) Genetic diversity of barley landrace accessions (Hordeum vulgare ssp. vulgare) conserved for different lengths of time in ex situ gene banks. Heredity (Edinb) 84: 476486.
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288295.
Ryder, EJ (1979) Spinach. In: Ryder, EJ (ed.) Leafy Salad Vegetables. New York, NY: Van Nostrand Reinhold, pp. 195227.
Smith, P (1976) Minor crops. In: Simmonds, NW (ed.) Evolution of Crop Plants. London: Longman, pp. 312313.
Sneep, J (1982) The domestication of spinach and the breeding history of its varieties. Euphytica(Suppl. 2): 127.
Takezaki, N and Nei, M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389399.
van der Vossen, HAM (2004) Spinacia oleracea L. In: Grubben, GJH and Denton, OA (eds) PROTA 2: Vegetables/Légumes. Wageningen: PROTA Plant Resources of Tropical Africa (CD-Rom).
van Hintum, TJL (2003) Molecular characterisation of a lettuce germplasm collection. In: van Hintum, TJL, Lebeda, A, Pink, DA and Schut, JW (eds) Proceedings of the Eucarpia Meeting on Leafy Vegetables Genetics and Breeding. Wageningen: Centre for Genetic Resources (CGN), pp. 99104.
van Hintum, TJL, van de Wiel, CCM, Visser, DL, van Treuren, R and Vosman, B (2007) The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects on diversity of regeneration, as measured with AFLPs. Theoretical and Applied Genetics 114: 777786.
Vavilov, NI (1992) Origin and Geography of Cultivated Plants, English edn. Cambridge: Cambridge University Press.
Ware, GW and McCollum, JP (1980) Spinach. In: Producing Vegetable Crops. 3rd edn. Danville, IL: Interstate Printers and Publishers, pp. 437449.


Type Description Title
Supplementary materials

Kuwahara et al. Supplementary Material
Tables and Figures

 PDF (303 KB)
303 KB

An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers

  • Kouhei Kuwahara (a1), Reimi Suzuki (a1), Yusuke Ito (a1), Tetsuo Mikami (a1) and Yasuyuki Onodera (a1)...


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed