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Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content

Published online by Cambridge University Press:  14 August 2015

Khaled Mirzaei  and
Ghader Mirzaghaderi
Khaled Mirzaei
Affiliation:
Department of Agronomy and Plant Breeding, University of Kurdistan, PO Box 416, Sanandaj, Iran
Ghader Mirzaghaderi*
Affiliation:
Department of Agronomy and Plant Breeding, University of Kurdistan, PO Box 416, Sanandaj, Iran
*
*Corresponding author. E-mail: gh.mirzaghaderi@uok.ac.ir
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Abstract

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

Keywords

genetic diversitypolymorphism information contentSimpson's diversity indexStart Codon Targeted polymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 1 , February 2017 , pp. 64 - 71
Copyright
Copyright © NIAB 2015 

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