Advertisement

Molecular Genetics and Genomics

, Volume 292, Issue 4, pp 847–855 | Cite as

Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

  • Şurhan Göl
  • Mehmet Göktay
  • Jens Allmer
  • Sami Doğanlar
  • Anne FraryEmail author
Original Article

Abstract

Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.

Keywords

Next generation sequencing Genomic SSRs Genetic diversity Microsatellites Population structure 

Notes

Acknowledgements

This research was supported by funding from an Izmir Institute of Technology Scientific Research Project, IYTE-BAP2012-2014.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards statement

This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

Sequence data are available at the SRA database of NCBI (SRX2266012).

Supplementary material

438_2017_1314_MOESM1_ESM.pdf (205 kb)
Supplementary material 1 (PDF 205 KB)

References

  1. Abuzayed M, El-Dabba N, Frary A, Doganla r S (2016) GDdom: an online tool for calculation of dominant marker gene diversity. Biochem Genet 43:1–3Google Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefPubMedGoogle Scholar
  3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9(3):208–218CrossRefGoogle Scholar
  4. Boswell VR (1949) Garden peas and spinach from the Middle East. Reprint of “Our Vegetable Travelers” Natl Geogr 96:2Google Scholar
  5. Cardle L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854PubMedPubMedCentralGoogle Scholar
  6. Chitwood J, Shi A, Mou B, Evans M, Clark J, Motes D, Chen P, Hensley D (2016) Population structure and association analysis of bolting, plant height, and leaf erectness in spinach. HortScience 51(5):481–486Google Scholar
  7. Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484):546–549CrossRefPubMedGoogle Scholar
  8. Doyle JJ, Doyle JE (1990) Isolation of plant DNA from fresh tissue. Focus (12):13–15Google Scholar
  9. Earl DA, Von Holdt BM (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361CrossRefGoogle Scholar
  10. Feng C, Bluhm BH, Correll JC (2015) Construction of a spinach bacterial artificial chromosome (BAC) library as a resource for gene identification and marker development. Plant Mol Biol Rep 33(6):1996–2005CrossRefGoogle Scholar
  11. Food and Agriculture Organization of the United Nati1ons, FAOSTAT (2013) http://www.fao.org/corp/statistics/en. Accessed 04 July 2016
  12. Hu J, Mou B, Vick BA (2007) Genetic diversity of 38 spinach (Spinacia oleracea L.) germplasm accessions and 10 commercial hybrids assessed by TRAP markers. Genet Resour Crop Evol 54(8):1667–1674CrossRefGoogle Scholar
  13. Ito M, Ohmido N, Akiyama Y, Fukui K, Koba T (2000) Characterization of spinach chromosomes by condensation patterns and physical mapping of 5 S and 45 S rDNAs by FISH. J Am Soc Hortic Sci 125(1):59–62Google Scholar
  14. Khattak JZK, Torp AM, Andersen SB (2006) A genetic linkage map of Spinacia oleracea and localization of a sex determination locus. Euphytica 148:311–318CrossRefGoogle Scholar
  15. Khattak JZK, Christiansen JL, Torp AM, Andersen SB (2007) Genic microsatellite markers for discrimination of spinach cultivars. Plant Breeding 126(4):454–456CrossRefGoogle Scholar
  16. Kuwahara K, Suzuki R, Ito Y, Mikami T, Onodera Y (2014) An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers. Plant Genet Resour 12(02):185–190CrossRefGoogle Scholar
  17. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359CrossRefPubMedPubMedCentralGoogle Scholar
  18. Lester GE, Makus DJ, Hodges DM, Jifon JL (2013) Summer (Subarctic) versus winter (Subtropic) production affects spinach (Spinacia oleracea L.) leaf bionutrients: Vitamins (C, E, Folate, K1, provitamin A), lutein, phenolics, and antioxidants. J Agric Food Chem 61(29):7019–7027CrossRefPubMedGoogle Scholar
  19. Ma J, Shi A, Mou B, Evans M, Clark JR, Motes D, Correll JC, Xiong H, Qin J, Chitwood J, Weng Y (2016) Association mapping of leaf traits in spinach (Spinacia oleracea L.). Plant Breeding 404:1–6Google Scholar
  20. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12CrossRefGoogle Scholar
  21. Minoche AE, Dohm JC, Schneider J, Holtgräwe D, Viehöver P, Montfort M, Sörensen TR, Weisshaar B, Himmelbauer H (2015) Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. Genome Biol 16(1):184CrossRefPubMedPubMedCentralGoogle Scholar
  22. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70(12):3321–3323CrossRefPubMedPubMedCentralGoogle Scholar
  23. Park YJ, Lee JK, Kim NS (2009) Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14(11):4546–4569CrossRefPubMedGoogle Scholar
  24. Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr
  25. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  26. Roldan-Ruiz I, Dendauw J, Bockstaele EV, Depicker A, Loose MD (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134CrossRefGoogle Scholar
  27. Shi A, Beiquan M, James CC (2016) Association analysis for oxalate concentration in spinach. Euphytica 212(1):17–28CrossRefGoogle Scholar
  28. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ BL (2009) AbySS: a paralel assembler for short read sequence data. Genome Res 19(6):1117–1123CrossRefPubMedPubMedCentralGoogle Scholar
  29. Yang XD, Tan HW, Zhu WM (2016) SpinachDB: a well-characterized genomic database for gene family classification and SNP information of spinach. PloS One 11(5):e0152706CrossRefPubMedPubMedCentralGoogle Scholar
  30. Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Şurhan Göl
    • 1
  • Mehmet Göktay
    • 1
  • Jens Allmer
    • 1
  • Sami Doğanlar
    • 1
  • Anne Frary
    • 1
    Email author
  1. 1.Department of Molecular Biology and GeneticsIzmir Institute of TechnologyUrla IzmirTurkey

Personalised recommendations