Alternative Splicing-Mediated Regulation of a novel allele of Badh2 Drives moderate Accumulation of 2-AP in Rice

Aroma is a crucial quality trait in rice, primarily regulated by the Badh2 gene located on chromo-some 8. In this study, we identified a novel allele of Badh2, badh2-I11, in an aromatic rice variety, Hei126 (H126). This allele carries a 55-bp deletion in intron 11 of the Badh2 gene, which leads to alternative splicing (AS), resulting in both normal and aberrant transcripts. The aberrant transcript contains a premature stop codon, leading to reduced Badh2 mRNA and moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of the F₂ population derived from a cross between H126 and a non-aromatic rice Huahang 48 (HH48) revealed a segregation ratio consistent with Mendelian inheritance (1:2:1), and the phenotypic ratio of aromatic to non-aromatic plants was 3:1. An InDel marker was developed for efficient screening of badh2-I11 in breeding population. This transitional phenotype highlights H126 as a unique moderate aromatic rice germplasm, accumulating 2-AP while retaining partial Badh2 function. This study provides novel insights into the molecular mechanism of aroma production via intron-mediated alternative splicing and offers valuable genetic resources and molecular tools for aromatic rice breeding.