Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)
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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.
KeywordsNext generation sequencing Genomic SSRs Genetic diversity Microsatellites Population structure
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.
Sequence data are available at the SRA database of NCBI (SRX2266012).
- 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
- Boswell VR (1949) Garden peas and spinach from the Middle East. Reprint of “Our Vegetable Travelers” Natl Geogr 96:2Google 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):481–486Google 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):546–549CrossRefPubMedGoogle Scholar
- Doyle JJ, Doyle JE (1990) Isolation of plant DNA from fresh tissue. Focus (12):13–15Google Scholar
- Food and Agriculture Organization of the United Nati1ons, FAOSTAT (2013) http://www.fao.org/corp/statistics/en. Accessed 04 July 2016
- 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
- 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
- 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
- Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr