Genetic differentiation using ISSR, SCoT and DNA barcoding for Quinoa genotypes

Quinoa is considered a good source of fiber, vitamins and minerals as well as health
benefiting phytochemicals. Molecular markers are essential tools to identify genetic diversity in 
different species and are useful for germplasm preservation and cultivar identification. The 
objectives of this study were to use different molecular markers to molecularly characterize seven 
quinoa genotypes using ISSR, SCoT and the DNA chloroplast markers of rbcL and rpoC1 to reveal 
genetic polymorphism and identify unique markers for each genotype. Fifteen of ISSR primers were 
used in this study, a total of 172 amplified bands were generated with an average of 11.7 bands 
/primer. A total number of amplified polymorphic bands of 90 with an average 6.0 bands /primer; 
the average level of polymorphism was 49.7%. The efficiency of ISSR markers in discriminating 
studied genotypes was estimated by obtaining the PIC values, where PIC values varied from 0.21 to 
0.84 with an average of 0.69. Twelve SCoT primers were employed to investigate the genetic 
polymorphism among the seven quinoa genotyping. A total of 157 amplified bands were generated 
by the 12 primers with an average of 13.1 bands /primer, while a total number of amplified 
polymorphic bands of 80 with an average of 6.7 band /primer, while the PIC values varied from 
0.50 to 0.84 with an average of 0.77. We successfully sequenced barcode genes of rbcL and rpoC1 
for the seven quinoa genotypes. These sequences have been submitted to NCBI respiratory and have 
been assigned to gene bank accession numbers. The sequence alignment revealed that, rbcL 
retrieved from studied quinoa genotypes with high similarity to other rbcL genes obtained from 
Chenopodium species by other studies, with similarities ranged from 76% to 80%. In addition, the 
rbcL gene displayed genetic similarity of high consistency with low genetic evolution and mutation. 
On the other hand, the sequence alignment revealed that, rpoC1 retrieved from studied quinoa 
genotypes with high similarity to other rpoC1 genes obtained from other plant species by other 
studies; similarities ranged from 80% to 81%.