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The present study was undertaken to develop a simple, robust, and reliable polymerase chain reaction-based molecular marker that can identify a critical nonsense mutation in a receptor like protein (RLP) gene of tomato. The  Solyc04g014400  locus was found to code for a RLP with leucine-rich repeats, a trans-membrane domain, and characteristic three-dimensional structure.  In silico  analysis revealed the gene to be  Pseudomonas -responsive. The gene was previously reported to contain a single nucleotide polymorphism (SNP) in the second exon, which converts the Trp 76 codon (TGG) to a premature stop (TAG) codon. Hence, a tetra-primer amplification refractory mutation system (T-ARMS) assay was developed to detect this functional SNP in 20 tomato genotypes in a co-dominant manner. Authenticity of the allele-specific amplicons was also tested, where the primers were observed to be discriminatory for the allelic variants. Suitability of the developed assay for determining heterozygosity in developed F 1  hybrids was also confirmed on the basis of the results. Thus, the developed T-ARMS marker will be useful for functional characterisation of this gene in the light of its  Pseudomonas -responsiveness.

the journal of horticultural science and biotechnology

Development of polymerase chain reaction-based marker for identification of a nonsense mutation in a  Pseudomonas -responsive receptor like protein gene of tomato