In Silico Design of PCR Primers to Amplify the Salt Tolerance Gene in Soybean

Florentina Kusmiyati, Sutarno Sutarno, Bagus Herwibawa

Abstract


Soybean yield is decreased because of many stresses such as salt stress. Ionic and osmotic stresses are the effects of salt stress. An effective way of maintaining sustainable production in salt-affected soil is through breeding high salt tolerance soybean, which can be detected by PCR. The optimal PCR plays an important role in gene expression analysis. The success of a PCR-based method largely depends on the optimal primer sequence analysis in silico prior to a wet-bench experiment. Here we described designing of primer using web-based tools. Many types of online primer design software are available, which can be used free of charge to design desirable primers. The objective was to design of PCR primers to amplify the salt tolerance gene in soybean. A highly conserved region of 411 bases was detected by Clustal Omega. Primers were predicted using Primer3 based on conserved region, considering ideal conditions for primer length, hairpin, dimer, Tm, and GC%. The predicted forward and reverse primers were validated using NetPrimer. Both forward and reverse primers have shown significant similarity with salt tolerance gene and recommended to be used to amplify the salt tolerance gene in soybean.

Keywords


FASTA, Glycine max, NCBI, NetPrimer, Primer3

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References


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DOI: https://doi.org/10.24203/ajas.v6i6.5532

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