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Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits

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Abstract

We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon’s information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species.

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Abbreviations

CITES :

Convention on International Trade in Endangered Species of Wild Fauna and Flora

MRA :

Multiple Association Analysis

PCoA :

Principal Coordinate Analysis

PIC :

Polymorphism Information Content

SEM :

Scanning Electron Microscope

UPGMA :

Un-weighted Paired Group Methods with Arithmetic Mean

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Acknowledgements

This work was financially supported by the Iran National Science Foundation [Grant No. 95826350] and the University of Kurdistan. The authors are thankful to Dr. Sirwan Babaie, Department of plant breeding and genetic, University of Kurdistan for photography of the orchid species.

Funding

The current work was financially supported by the Iran National Science Foundation [grant No. 95826350] and the University of Kurdistan, Iran.

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Authors and Affiliations

  1. Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175, Sanandaj, Iran

    Soheila Gholami, Yavar Vafaee & Farzad Nazari

  2. Medicinal Plants Breeding and Development Research Institute, University of Kurdistan, 66177-15175, Sanandaj, Iran

    Yavar Vafaee

  3. Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden

    Abdolbaset Ghorbani

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  1. Soheila Gholami
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Correspondence to Yavar Vafaee.

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Gholami, S., Vafaee, Y., Nazari, F. et al. Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits. Physiol Mol Biol Plants 27, 769–785 (2021). https://doi.org/10.1007/s12298-021-00978-4

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