Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)
| Autor: | Anne Frary, Jens Allmer, Sami Doganlar, Şurhan Göl, Mehmet Göktay |
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| Přispěvatelé: | TR107974, TR1977, TR114553, Göl, Şurhan, Göktay, Mehmet, Allmer, Jens, Doğanlar, Sami, Frary, Anne, Izmir Institute of Technology. Molecular Biology and Genetics |
| Rok vydání: | 2016 |
| Předmět: |
0106 biological sciences
0301 basic medicine Germplasm Genetic Markers DNA Plant Biology Population structure 01 natural sciences Genetic diversity DNA sequencing 03 medical and health sciences Gene mapping Spinacia oleracea Next generation sequencing Botany Genetics Microsatellites Molecular Biology Contig Base Sequence Geography food and beverages Chromosome Mapping Genetic Variation High-Throughput Nucleotide Sequencing General Medicine Sequence Analysis DNA biology.organism_classification 030104 developmental biology Genetic marker Genomic SSRs Spinach Microsatellite Genome Plant 010606 plant biology & botany Microsatellite Repeats |
| Zdroj: | Molecular genetics and genomics : MGG. 292(4) |
| ISSN: | 1617-4623 |
| Popis: | 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. Izmir Institute of Technology Scientific Research Project, IYTE-BAP |
| Databáze: | OpenAIRE |
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