Alternative splicing-mediated regulation of a novel allele of Badh2 drives moderate accumulation of 2-AP in rice.

Key message: A novel allele of Badh2, badh2-I11 undergoes alternative splicing and leads to reduced Badh2 expression and enhanced 2-AP accumulation in rice. Aroma is a crucial quality trait in rice and is primarily regulated by the Badh2 gene located on chromosome 8. In this study, we identified a novel allele of Badh2, badh2-I11, in the aromatic rice variety, Hei126 (H126). This allele harbors a 55-bp deletion in intron 11, inducing alternative splicing, that generates both wild-type transcripts and aberrant transcripts containing a premature stop codon. Consequently, Badh2 mRNA levels are reduced, leading to moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of an F₂ population derived from a cross between Huahang 48 (non-aromatic, Badh2/Badh2) and H126 (aromatic, badh2-I11/badh2-I11) revealed a genotypic segregation ratio 1:2:1 (Badh2/Badh2: Badh2/badh2-I11: badh2-I11/badh2-I11), consistent with Mendelian inheritance for a single codominant locus. The corresponding phenotypic ratio of non-aromatic to aromatic plants was 3:1. We developed a codominant InDel marker for efficient screening of badh2-I11 in breeding populations. This intermediate aromatic phenotype establishes H126 as a unique germplasm resource, accumulating 2-AP while retaining partial Badh2 function. Our findings elucidate a novel molecular mechanism of aroma production mediated by intronic alternative splicing and provide valuable genetic resources and molecular tools for aromatic rice breeding.