E-microsatellite markers for some naturally occurring Salvia species in the Mediterranean region

The genus Salvia L. contains about 1000 species, more than 40 of which are endemic to the Mediterranean region. Species boundaries and classifications of this genus have been mainly conducted based on morphological and anatomical characteristics. Although genomic and genic microsatellites are commonly used in a variety of genetic studies in many plant and animal species, their use has been limited in Salvia species. This research was undertaken to study microsatellite contents of expressed sequence tags (ESTs) and develop a new set of expressed-microsatellite (e-microsatellite) markers using the GenBank databases. In in silico studies of the research, microsatellites were identified and e-microsatellite primer pairs flanking the repeats were designed. In in vitro studies of the present work, e-microsatellite primer pairs were used to amplify genomic DNA samples of different Salvia species naturally occurring in the Mediterranean region of Turkey. The results indicated that ESTs of related species deposited in GenBank were reliable sources for the development of e-microsatellite markers. The results of this study also indicated that cross-transferability of e-microsatellite markers decreased as the evolutionary distance among the tested Salvia species increased. E-microsatellite loci presented in this work could be very useful for measuring genetic diversity, gene flow, and species identification studies in the genus Salvia.

Anahtar Kelimeler:

Cross-transferability, DNA markers, expressed sequence tags, Labiatae, sage, touch-down-PCR

E-microsatellite markers for some naturally occurring Salvia species in the Mediterranean region

Keywords:

Cross-transferability, DNA markers, expressed sequence tags, Labiatae, sage, touch-down-PCR,

PDF

___

Bilgen M, Karaca M, Onus AN, Ince AG (2004). A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. Bioinformatics 20: 3379 –3386.
Deng KJ, Zhang Y, Ren YL (2009). Identification, characteristics, and utilization of simple sequence repeat markers derived from Salvia miltiorrhiza. Acta Pharm Sinic 44: 1165–1172.
Duran C, Singhania R, Raman H, Batley J, Edwards D (2013). Predicting polymorphic EST-SSRs in silico. Mol Ecol Resour 13: 538–545.
Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004). One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108: 1392–400.
Ince AG (2012). Contig-based microsatellite marker approach and its application in Cichorium ESTs. Rom Biotech Lett 17: 7177– 7186.
Ince AG, Karaca M (2009). The MAGi RNA extraction method: a highly efficient and simple procedure for fresh and dry plant tissue. J Sci Food Agr 89: 168–176.
Ince AG, Karaca M (2012). Species-specific touch-down DAMD- PCR markers for Salvia species. J Med Plants Res 6: 1590–1595.
Ince AG, Karaca M, Bilgen M, Onus AN (2008). Digital differential display tools for mining microsatellite containing organism, organ, and tissue. Plant Cell Tiss Org 94: 281–290.
Ince AG, Karaca M, Onus AN (2010a). Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28: 285–291.
Ince AG, Karaca M, Onus AN (2010b). CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Mol Breeding 25: 491–499.
Ince AG, Karaca M, Onus AN (2010c). Differential expression patterns of genes containing microsatellites in Capsicum annuum L. Mol Breeding 25: 645–658.
Ince AG, Yildiz F, Karaca M (2011). The MAGi DNA extraction method for fresh tissues and dry seeds. J Med Plants Res 5: 5458–5464.
Karaca M, Bilgen M, Onus AN, Ince AG, Elmasulu SY (2005a). Exact tandem repeats analyzer (E-TRA) for DNA sequence mining. J Genet 84: 49–54.
Karaca M, İnce AG (2011). New non-redundant microsatellite and CAPS-microsatellite markers for cotton (Gossypium L.). Turk J Field Crops 16: 172–178.
Karaca M, Ince AG, Ay ST, Turgut K, Onus AN (2008). PCR-RFLP and DAMD-PCR genotyping for Salvia species. J Sci Food Agr 88: 2508–2516.
Karaca M, Ince AG, Aydin A, Ay ST (2013). Cross-genera transferable e-microsatellite markers for 12 genera of the Lamiaceae family. J Sci Food Agr 93: 1869–1879.
Karaca M, Ince AG, Elmasulu SY, Onus AN, Turgut K (2005b). Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Anal Biochem 343: 353–355.
Karaca M, Saha S, Callahan FE, Jenkins JN, Read JJ, Percy RG (2004). Molecular and cytological characterization of a cytoplasmic- specific mutant in pima cotton (Gossypium barbadense L.). Euphytica 139: 187–197.
Karan M, Evans DS, Reilly D, Schulte K, Wright C, Innes D, Holton TA, Nikles DG, Dickinson GR (2012). Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Mol Ecol Resour 12: 344–353.
Mishra RK, Gangadhar BH, Yu JW, Kim DH, Park SW (2011). Development and characteristics of EST based SSR markers in Madagascar periwinkle (Catharanthus roseus) and their transferability in other medicinal plants. Plant Omics 4: 154– 162.
Polat E, Ince AG, Karaca M, Onus AN (2010). Mining and utilization of mushroom ESTs for microsatellites. Conserv Genet 11: 1123–1126.
Radosavljevic I, Jakse J, Javornik B, Satovic Z, Liber Z (2011). New microsatellite markers for Salvia officinalis (Lamiaceae) and cross-amplification in closely related species. Am J Bot 98: e316–e318.
Radosavljevic I, Satovic Z, Jakse J, Javornik B, Greguras D, Jug-Dujakovic M, Liber Z (2012). Development of new microsatellite markers for Salvia officinalis L. and its potential use in conservation-genetic studies of narrow endemic Salvia brachyodon Vandas. Int J Mol Sci 13: 12082–12093.
Rozen S, Skaletsky H (2000). PRIMER 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S, editors. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ, USA: Humana Press, pp. 365–386.
Sim SC, Yu JK, Jo YK, Sorrells ME, Jung G (2009). Transferability of cereal EST-SSR markers to ryegrass. Genome 52: 431–437.
Teacher AGF, Kahkonen K., Merila J (2012). Development of 61 new transcriptome-derived microsatellites for the Atlantic herring (Clupea harengus). Conserv Genet Res 4: 71–74.
Walker JB, Sytsma KJ (2007). Staminal evolution in the genus Salvia (Lamiaceae): molecular phylogenetic evidence for multiple origins of the staminal lever. Ann Bot 100: 375–391.
Walker JB, Sytsma KJ, Treutlein J, Wink M (2004). Salvia (Lamiaceae) is not monophyletic: implications for the systematic, radiation, and ecological specializations of Salvia and tribe Mentheae. Am J Bot 91: 1115–1125.
Wang Y, Ren R, Yu Z (2008). Bioinformatics mining of EST-SSR loci in the Pacific oyster, Crassostrea gigas. Anim Genet 39: 287– 289.
Xu G, Liu C, Huang L, Wang X, Zhang Y, Liu S, Liao C, Yuan Q, Zhou X (2013). Development of new EST-derived SSRs in Salvia miltiorrhiza (Labiatae) in China and preliminary analysis of genetic diversity and population structure. Biochem Syst Ecol 51: 308–313.