COBRA gene is involved in the regulation of cellulose deposition and orientation of cell expansion. Any single nucleotide differences may influence the functions of this gene. Hence, this study was carried out to isolate the COBRA partial genomic sequence and subsequently, to determine the nucleotide variation of COBRA gene in Neolamarckia cadamba. N. cadamba, also locally known as kelampayan is one of the fast-growing deciduous and indigenous tree species with great commercial values. The targeted DNA sequence of COBRA gene was amplified with the designed primer by using Polymerase Chain Reaction (PCR) technique. The 517 bp of COBRA partial genomic sequence was subjected to BLASTn analysis to search for homology sequence and validate the identity of the obtained sequence through NCBI. Multiple alignment was carried out by ClustalW for manual detection of single nucleotide polymorphisms (SNPs). Five SNPs were detected in the exon region and two SNPs in the intron region of COBRA partial genomic sequences. Of these five detected SNPs, four non-synonymous mutations and one synonymous mutation were discovered in the COBRA amino acid sequences. Based on the in silico restriction analysis, one possible restriction enzyme, HpyCH4III was detected for SNP at nucleotide 384 bp of a sample which could be useful for genetic marker development, such as CAPS marker through detection of SNPs is essential in the efforts of genotyping project.

Key words: Neolamarckia cadamba, polymerase chain reaction (PCR), COBRA gene, single nucleotide polymorphisms (SNPs), molecular markers