The origin and evolution of fragrance in rice ( <i>Oryza sativa</i> L.)

<jats:p> Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene ( <jats:italic>BADH2</jats:italic> ) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the <jats:italic>BADH2</jats:italic> gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, <jats:italic>badh2.1</jats:italic> , is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the <jats:italic>badh2.1</jats:italic> allele within the <jats:italic>Japonica</jats:italic> varietal group and demonstrate the introgression of this allele from <jats:italic>Japonica</jats:italic> to <jats:italic>Indica</jats:italic> . Basmati-like accessions were nearly identical to the ancestral <jats:italic>Japonica</jats:italic> haplotype across a 5.3-Mb region flanking <jats:italic>BADH2</jats:italic> regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the <jats:italic>Japonica</jats:italic> gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the <jats:italic>Indica</jats:italic> varietal group. </jats:p>