Designing Specific Primers to Study Single Nucleotide Diversity (SNP) of Genes and to Determine their Performance

There is a lot of information about genes sequence but their functions are still unknown. So, to fill the gap between structure and function of these sequences many reverse genetic researches have been done. Current experiment studying, how to design gene-specific primers, that can determine single nucleotide diversity and its impact on gene function.This research was condacted at International Center for Agricultural Research in the Dry Areas (ICARDA). Genes studied in present experiment include two genes responsible for salinity tolerance in barley, CBL4 and HvHKT1, in which eight primer pairs were designed. Primers efficiency for amplification of desired regions and demonstration of the single nucleotide variation was assessed through polymerase chain reaction and sequencing the fragments. All primers were designed with high function for amplification of genomic fragments and the associated single nucleotide diversity. These specific primers were designed from gene coding regions. They can therefore help to study nucleotide diversity between different genotypes and their roles in changes in gene function. Also, selection based on gene-specific markers would be more efficient than linked markers.