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Genetic Variation and Structure in Natural Populations of a Medicinal Vegetable, Satureja bachtiarica, Inferred from Microsatellite Markers Developed Using Next-Generation Sequencing

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Abstract

Satureja bachtiarica Bunge (Lamiaceae) is a medicinal plant native to Iran which is widely used in traditional medicine, as a spice and as a vegetable. Understanding the patterns of genetic variation and structure of natural populations of the plant will be crucial for breeding and management purposes. However, until now, there has been no molecular tool with codominance inheritance available for studying genetic variation in this plant. In this study, we developed microsatellite markers for S. bachtiarica using a next-generation sequencing technique, and applied these markers to quantify the genetic variation and structure of natural populations. Sixty individuals collected from five natural populations were tested with 15 markers, 11 of which were fund to be polymorphic. The number of alleles per locus ranged from 4 to 17, with an average of 7.5 alleles per locus. The polymorphic information content of loci ranged from 0.41 to 0.89, with an average of 0.63. The average observed and expected heterozygosities over all populations were 0.62 (range 0.58 to 0.69) and 0.61 (range 0.60 to 0.63), respectively, and a low level of inbreeding (FIS) was observed in all populations (ranging from − 0.08 to 0.10) except Boli. None of the populations revealed any signature of recent reduction in population size. Private allelic richness was positively correlated with elevation (P < 0.05). The mean pairwise FST (± SD) among populations was 0.07 ± 0.01 (range 0.05 to 0.10). The clustering and Bayesian structure analyses exhibited genetic admixture between populations as supported by a weak population differentiation. The results of this study show the high efficiency of developed markers to investigate the genetics of natural populations of S. bachtiarica. The developed markers can also help to screen natural variation in diverse populations of closely related species, and can consequently be applied in conservation genetic and breeding programs.

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Acknowledgments

Authors thank Dr. Sverre Lundemo for his valuable comments and efforts to improve the language of the final version of the manuscript.

Funding

This research is supported by a grant no. PHD95100659 from the Iran National Science Foundation (INSF).

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Authors and Affiliations

  1. Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran

    Rahil Movahedi, Abdolali Shojaeiyan & Mahdi Ayyari

  2. Department of Plant Sciences, School of Biology, College of Science, University of Tehran, 14155-6455, Tehran, Iran

    Mohsen Falahati-Anbaran

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  1. Rahil Movahedi
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  2. Abdolali Shojaeiyan
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  3. Mohsen Falahati-Anbaran
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  4. Mahdi Ayyari
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Correspondence to Abdolali Shojaeiyan.

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Movahedi, R., Shojaeiyan, A., Falahati-Anbaran, M. et al. Genetic Variation and Structure in Natural Populations of a Medicinal Vegetable, Satureja bachtiarica, Inferred from Microsatellite Markers Developed Using Next-Generation Sequencing. Plant Mol Biol Rep 37, 14–23 (2019). https://doi.org/10.1007/s11105-018-1126-7

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