Sequence polymorphism in the 7^th exon of Badh2 gene in short grain aromatic bengal land races of rice (Oryza sativa L.)

Aroma in rice is associated with increased level of 2-acetyl-1-pyrroline (2AP) controlled by a recessive gene (fgr) located on chromosome 8 encoding betaine aldehyde dehydrogenase 2 (BADH2). An eight bp deletion and three single nucleotide polymorphisms (SNPs) in badh2 gene presumably disable the BADH2 enzyme which results in accumulation of the fragrant compound, 2-acetyl-1-pyrroline (2AP) in fragrant rice. The present study was undertaken to analyze allelic variation of the 7^th exon of badh2 gene in four short grain aromatic land races of Bengal (Gobindobhog, Radhunipagal, Khaskani and Tulaipanji). A ∼580 bp DNA fragment was amplified covering 7^th exon region and sequenced. Partial gene sequence of all aromatic rice revealed one 8 bp deletion and three SNPs in exon 7 of fgr gene. However, an additional 4 bp deletion just upstream to the 8 bp deletion regions was observed in Gobindobhog, most popular aromatic land race of Bengal.