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

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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.

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References

  • Abuzayed M, El-Dabba N, Frary A, Doganla r S (2016) GDdom: an online tool for calculation of dominant marker gene diversity. Biochem Genet 43:1–3

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9(3):208–218

    Article  CAS  Google Scholar 

  • Boswell VR (1949) Garden peas and spinach from the Middle East. Reprint of “Our Vegetable Travelers” Natl Geogr 96:2

    Google Scholar 

  • Cardle L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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):481–486

    Article  CAS  Google Scholar 

  • 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):546–549

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JE (1990) Isolation of plant DNA from fresh tissue. Focus (12):13–15

  • Earl DA, Von Holdt BM (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • 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):1996–2005

    Article  CAS  Google Scholar 

  • Food and Agriculture Organization of the United Nati1ons, FAOSTAT (2013) http://www.fao.org/corp/statistics/en. Accessed 04 July 2016

  • 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):1667–1674

    Article  CAS  Google Scholar 

  • 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):59–62

    Article  CAS  Google Scholar 

  • Khattak JZK, Torp AM, Andersen SB (2006) A genetic linkage map of Spinacia oleracea and localization of a sex determination locus. Euphytica 148:311–318

    Article  CAS  Google Scholar 

  • Khattak JZK, Christiansen JL, Torp AM, Andersen SB (2007) Genic microsatellite markers for discrimination of spinach cultivars. Plant Breeding 126(4):454–456

    Article  CAS  Google Scholar 

  • 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):185–190

    Article  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):7019–7027

    Article  CAS  PubMed  Google Scholar 

  • 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 404:1–6

    Google Scholar 

  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12

    Article  Google Scholar 

  • 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):184

    Article  PubMed  PubMed Central  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70(12):3321–3323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):4546–4569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roldan-Ruiz I, Dendauw J, Bockstaele EV, Depicker A, Loose MD (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134

    Article  CAS  Google Scholar 

  • Shi A, Beiquan M, James CC (2016) Association analysis for oxalate concentration in spinach. Euphytica 212(1):17–28

    Article  CAS  Google Scholar 

  • 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):1117–1123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):e0152706

    Article  PubMed  PubMed Central  Google Scholar 

  • 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):193–208

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla Izmir, 35430, Turkey

    Şurhan Göl, Mehmet Göktay, Jens Allmer, Sami Doğanlar & Anne Frary

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  1. Şurhan Göl
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  2. Mehmet Göktay
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  3. Jens Allmer
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  4. Sami Doğanlar
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  5. Anne Frary
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Correspondence to Anne Frary.

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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).

Additional information

Communicated by S. Hohmann.

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Supplementary material 1 (PDF 205 KB)

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Göl, Ş., Göktay, M., Allmer, J. et al. Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea). Mol Genet Genomics 292, 847–855 (2017). https://doi.org/10.1007/s00438-017-1314-4

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  • DOI: https://doi.org/10.1007/s00438-017-1314-4

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