Economizing marker assisted selection through cost-effective assay of sd1 gene in rice (Oryza sativa)

PCR amplification and detection of GC rich sequences in DNA is a challenge due to formation secondary structures which resist denaturation, thereby stalling Taq polymerases as well affecting primer annealing. Presently, high fidelity polymerase used for amplifying long GC-rich fragments, while dimethyl sulfoxide (DMSO) has also been suggested an additive Polymerase Chain Reaction (PCR) mix avoid templates containing content. In the present study, efficiency normal with 5% DMSO compared applied better fragments content sd1 gene rice. Normal displayed reproducible results platinum sd1, successfully detecting dominant wild type allele governing tall plant height from recessive semi-dwarf allele. There were no adverse effects amplified improved significantly indicating improvement efficiency. The modified protocol including provides cost effective cheaper alternative reliable assessment genomic differences GCrich regions gene. This will help eliminating need costly polymerase, helping economizing marker assisted selection.