Development of a CAPS marker for the badh2.7 allele in Sri Lankan fragrant rice (Oryza sativa)

Abstract

Fragrance in rice is caused by mutations in the badh2 (betaine aldehyde dehydrogenase) gene. It was previously reported that exons 1, 2, 7, 10, 13 and 14 of badh2 are hot spots for various mutations leading to fra grance in most aromatic rice. This study was carried out to sequence the 14th exon of badh2 gene of Sri Lankan aromatic rice varieties that lack the badh2.1 allele. The aims of the study were to predict the aberrant protein structure and to develop a functional DNA marker. In view of this, we sequenced the 14th exon of four traditional aromatic accessions and compared with a published sequence. Four accessions contained a nucleotide ‘G’ insertion in the 14th exon. This novel mutation can be classified as the badh2.7 allele. The predicted three-dimensional protein structure of the mutant shows loss of part of the oligomerization and coenzyme binding domains, a change that is predicted to result in fra grance. A CAPS-based novel marker, Bad2.7CAPS, was developed to identify varieties possessing this badh2.7 allele, and it can be utilized in rice breeding programmes.