Conversion of barley SNPs into PCR-based markers using dCAPS method

Molecular genetic research relies heavily on the ability to detect polymorphisms in DNA. Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation in the genome. In combination with a PCR assay, the corresponding SNP can be analyzed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. The dCAPS method exploits the well-known specificity of a restriction endonuclease for its recognition site and can be used to virtually detect any SNP. Here, we describe the use of the dCAPS method for detecting single-nucleotide changes by means of a barley EST, CK569932, PCR-based marker.     

Studying Genetic Variability of Pomegranate (Punica granatum L.) Based on Chloroplast DNA and Barcode Genes

Chloroplast DNA has been used extensively to analyze plant phylogenies at different taxonomic levels because of its size, organization and sequence conservation. In the present research, two chloroplastic regions, petA–psaJ, trnC–trnD and four DNA barcodes (trnH–psbA, ITS, rbcL, matK), were used to introduce suitable regions for the assessment of genetic diversity among P. granatum L. genotypes. Analysis of psbE–petL in petA–psaJ region revealed 1,300 nucleotides with 4.29 % genetic diversity among genotypes, while trnC–petN in trnC–trnD region showed 1.8 % genetic diversity. Therefore, despite the results obtained from the study of other plants, the trnC–trnD region had a low potential for the evaluation of diversity among pomegranate genotypes. Analysis of DNA barcodes in pomegranate showed that trnH–psbA (genetic diversity 2.91 %) provides the highest intra-species variation, followed by ITS (genetic diversity 0.44 %). Eighteen genotypes from different geographical origins of Iran were used to investigate psbE–petL and trnH–psbA potential as novel barcodes to determine genetic polymorphism and characterize pomegranate genotypes. The results suggested that two regions, psbE–petL and trnH–psbA, were more suitable for determining intra-species relationships of pomegranate.