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

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We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including (L.) R. M. Bateman, Pridgeon and M. W. Chase, (Kar. & Kir.) Nevski, (Boiss.) Schltr., Banks and Solander, (L.) L., Lam., Bornm. and Fleischm., and 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 () varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles () (1.13) and effective number of alleles () (1.09). At the same time, the highest (1.29) and (1.18) values were obtained in collected from Javanrood (Oyst.JA). Shannon's information index () was ranged from 0.03 for accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population ( accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient ( = 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.