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Population Genetic and Structure Analyses of Annual Iranian Medicago orbicularis Indicates Advantageous Use of HTS-Generated SSR Markers

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Abstract

Simple sequence repeat (SSR) markers are among more reliable markers widely used in population genetics and traditionally need intensive labor to develop. High-throughput sequencing (HTS) has enabled researches in screening whole DNA in order to develop dozens of reliable SSR markers to pave route for future studies. Annual medics (Medicago spp.) are specifically beneficial in agriculture, genetics, and pastureland management plans. In order to facilitate study of annual medics using SSRs and to test their effectiveness, HTS screening of whole DNA resulted in developing of hundreds of primer pairs published in this paper. Subsequent testing of candidate primers on Iranian M. orbicularis germplasm was narrowed down to six more variable primer pairs that generated 28 polymorphic bands with the allele size of 200–310 bp. Eleven populations were examined using our SSR markers. The average polymorphic information content was very high (> 0.90) for the primer combinations. Genetic diversity parameters were measured for all populations. A high level of polymorphism of 75% within populations was observed. We hypothesized that the self-pollinating reproductive system of M. orbicularis has led to the reduction of gene flow between populations and ultimately the low diversity among populations (24%). Different genotypes observed by structure analysis as well as regression and correlation analyses showed that genetical similarity was congruent with the geographical proximity. Our results suggest that our HTS-generated SSR markers can be used for the further study of other annual medics.

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Data Availability

The data that support the findings of this study are openly available from the corresponding author, IM, upon reasonable request.

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Authors and Affiliations

  1. Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran

    Zahra Morshedi & Iraj Mehregan

  2. Department of Botany, Agricultural Research Education and Extension Organization (AREEO), Research Institute of Forests and Rangelands, Tehran, Iran

    Mostafa Assadi

  3. Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada

    Ernest Small

  4. Department of Biology, Islamic Azad University, Borujerd Branch, Borujerd, Iran

    Mohammad Mehdi Dehshiri

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  1. Zahra Morshedi
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  2. Mostafa Assadi
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  3. Ernest Small
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  5. Iraj Mehregan
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Contributions

IM and ES proposed the main idea. ZM in collaboration with IM performed the fieldworks and formal analysis. Software analysis were done by ZM. MA and MD identified the plant samples. ZM, ES and IM contributed in writing the manuscript. All authors read and approved the final manuscript.

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Correspondence to Iraj Mehregan.

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Morshedi, Z., Assadi, M., Small, E. et al. Population Genetic and Structure Analyses of Annual Iranian Medicago orbicularis Indicates Advantageous Use of HTS-Generated SSR Markers. Iran J Sci 48, 331–342 (2024). https://doi.org/10.1007/s40995-024-01597-w

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