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

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-021-00978-4.

Keywords: Conservation; Iranian orchids; Population structure; RET species; SCoT.

Fig. 1

Geographic locations and collection sites of the sample populations and inflorescence of studied terrestrial orchid species. a Dactylorhiza umbrosa (Kar. & Kir.) Nevski, b Himantoglossum affine (Boiss.) Schltr., c Orchis simia Lam., d Orchis mascula (L.) L., e Anacamptis coriophora (L.) R.M.Bateman, Pridgeon & M.W.Chase, f Ophrys schulzei Bornm. & Fleischm., g Ophrys straussii H. Fleischm. & Bornm., h Orchis collina Banks and Solander

Fig. 2

Seed morphology, view in light microscopy and SEM. a Dactylorhiza umbrosa, b Himantoglossum affine, c Orchis mascula, d Orchis simia, e Anacamptis coriophora, f Ophrys schulzei, g Ophrys straussii, h Orchis collina

Fig. 3

UPGMA dendrogram of genetic similarity based on the SCoT data generated from Jaccard coefficients

Fig. 4

The PCoA biplot of terrestrial orchid populations based on the two first principal coordinates (PCo1 = 39.40%, PCo2 = 30.76%) using SCoT data

Fig. 5

Population structure of 97 Iranian terrestrial orchids based on SCoT data analyzed by STRUCTURE software and Bayesian model. a K = 7; b K = 8; c K = 9. Number of each horizontal lane is the individual code and each color shows a subpopulation