In silico sequence analysis of Gibberellin-20 Oxidase-2, the semidwarfing protein of rice through the application of BLAST, FASTA and WU-Blast 2 programs.

The semidwarfing gene in rice (sd-1) is one of the most important genes deployed in modern rice breeding. Its recessive character results in a shortened culm with improved lodging resistance and a greater harvest index, allowing for the increased use of nitrogen fertilizers. The sd-1 gene was first identified in the Chinese variety Dee-geo-woo-gen (DGWG), and was crossed in the early 1960s with Peta (tall) to develop the semidwarf cultivar IR8, which produced record yields throughout Asia and formed the basis for the development of new highyielding, semidwarf plant types (IRRI, 1967). Plant architecture refers to the collection of all important agronomic characters which determines the grain production. In rice it is mainly affected by plant height, tillering and panicle morphology (Wang et al., 2005). In rice, short stature plants were developed by altering the plant architecture. Short stature in rice was developed by a recessive semidwarfgene sd-1, responsible for high yielding varieties (Nagano et al., 2005). The sd-1 gene codes for the oxidase enzyme involved in the biosynthesis of gibberellins, Gibberellin-20 oxidase-2(GA20ox2). GA20ox2 is tightly linked to the sd-1 locus of rice chromosome 1. Semidwarfing gene inhibits the elongation of lower internodes which makes rice resistant oto lodging (Ogi et al.,1993). The short stature of IR8 is due to a mutation in the plant’s sd1 gene, encoding an oxidase enzyme involved in the biosynthesis of gibberellin, a plant growth hormone (Sasaki et al., 2002). Ga20ox2 catalyses the conversion of GA 53 to GA 20 . DGWG sd-1 mutants have 383 bp deletion in genomic sequence which encode a non-functional protein in an indica semidwarf IR8 (Monna et al., 2002). However, a substitution of Leu266 that is highly conserved residue resulted in the loss of function in japonica semidwarf. Rice represents enormous gene pool for improvement of rice cultivars as well as other crops which show significant similarity to rice genome. By making the use of sequence similarity/ homology genetic relationships among cereal crops can be established (Ishii et al., 1996). Comparative genomic analysis revealed that the sdw1/denso gene that controls plant height, yield and quality has located in the syntenic region of the rice semidwarf gene sd1 on chromosome 1 (Jia et al., 2009). Protein sequences contain valuable information to predict structure and function of gene product. The comparison of two sets is a fundamental task that infers about how two sequences may be related functionally and genetically. The simultaneous alignment of amino acid sequences is now a major tool in molecular biology. The advent of large genome projects led to an explosion of Correspondence to: ASTHA DUHAN, Department of Bioinformatics, Mata Gujri College, FATEHGARH SAHIB (PUNJAB) INDIA Authors’ affiliations: MANOJ KUMAR SHARMA, Department of Bioinformatics, Janta Vedi College, Baraut, BAGHPAT (U.P.) INDIA TAVINDERJEET KAUR, Department of Bioinformatics, Mata Gujri College, FATEHGARH SAHIB (PUNJAB) INDIA