Genomic Sequence and Polymorphisms of a Rice Chitinase Gene, Cht4

Abstract

A novel chitinase was identified in a rice EST Iibrary based on a partial polypeptide sequence of a putative dormancy-related protein in rice husk and its genetic locus was detected on chromosome 4. Thereafter, the whole genomic sequence of Cht4 was determined by using TAIL-PCR based on cDNA sequence data. A full sequence of the protein encoded by Cht4 was confirmed to be significantly shorter than that of known rice chitinases, and to have a unique primary structure. The 5' flanking sequence of about 700 bp was also determined and compared with that of known chitinases. Besides a common intron in the sequence there is a polymorphism in the 3' flanking region for an inserted sequence which is similar to the Wanderer element, one of the transposons. The insertion was observed only in Indica cultivars.