Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2)

Abstract

The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD.