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Key message <p><b>A novel allele of</b> <Emphasis Type="BoldItalic">Badh2</Emphasis>, <Emphasis Type="BoldItalic">badh2-I11</Emphasis> <b>undergoes alternative splicing and leads to reduced</b> <Emphasis Type="BoldItalic">Badh2</Emphasis> <b>expression and enhanced 2-AP accumulation in rice</b>.</p> Abstract <p>Aroma is a crucial quality trait in rice and is primarily regulated by the <i>Badh2</i> gene located on chromosome 8. In this study, we identified a novel allele of <i>Badh2</i>, <i>badh2-I11,</i> 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, <i>Badh2</i> mRNA levels are reduced, leading to moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of an F<sub>2</sub> population derived from a cross between Huahang 48 (non-aromatic,&#xa0;<i>Badh2/Badh2</i>) and H126&#xa0;(aromatic,&#xa0;<i>badh2-I11/badh2-I11</i>) revealed a genotypic segregation ratio 1:2:1&#xa0;(<i>Badh2/</i><i>Badh2</i>: <i>Badh2/badh2-I11</i>: <i>badh2-I11/badh2-I11</i>), 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 <i>badh2-I11</i> in breeding populations. This intermediate aromatic phenotype establishes H126 as a unique germplasm resource, accumulating 2-AP while retaining partial <i>Badh2</i> 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.</p>

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

  • 期刊论文

  • 发表日期：

    2025年8月1日

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  • Xueyu Liang,
  • Ying Chen,
  • Kai Liu,
  • Min Guo,
  • Danhua Zhou,
  • Cuihong Huang,
  • Tao Guo,
  • Hui Wang,
  • Guili Yang

摘要

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.

Abstract

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.