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<p>Fragrant rice, renowned for its superior grain characteristics and distinct aroma, commands a premium price in Indian and international markets. Aromatic rice genotypes have been shown to harbour a truncated version of the <i>Betaine aldehyde dehydrogenase 2</i> (<i>badh2</i>) gene located on chromosome 8, which is responsible for fragrance production. In this study, we assessed Kashmir Himalayan rice genotypes (Mushk Budji, Jehlum and Kawa Kreed) and aromatic long-slender grain rice Pusa Sugandh-3 for allelic variations in exon 2 of the <i>badh2</i> gene. Primers targeting exon 2 were designed based on previous research and successfully amplified a 200–207&#xa0;bp fragment across the genotypes. The analysis revealed the presence of a 7-bp deletion (“CGGGCGC”), a 2-bp deletion (“AA”), and two single nucleotide polymorphisms (“CC”) in the <i>badh2</i> exon 2 of the aromatic Mushk Budji genotype and 7-bp deletion (“CGGGCGC”) along with four single nucleotide polymorphisms (C, G, T, G → G, A, G, C) in Pusa Sugandh-3. This is the first report of these specific deletions and SNPs in these genotypes. Additionally, the ALU-I functional marker was used to confirm these variations, revealing distinct restriction patterns in aromatic cultivars, with cleaved fragments (158&#xa0;bp and 322&#xa0;bp) in Mushk Budji and Pusa Sugandh-3, and an intact 480&#xa0;bp fragment in non-aromatic cultivars. No such variations were observed in non-aromatic rice cultivars. These findings provide valuable insights into the genetic basis of aroma in rice genotypes and could be utilised for crop improvement programs targeting aromatic rice traits.</p>

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First report on molecular validation for aroma in Mushk Budji and Pusa Sugandh-3: allelic variations and deletions in the Exon 2 of BADH2 Gene

  • 期刊论文

  • 发表日期：

    2026年1月5日

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  • Yaseen Sofi,
  • Komaljeet Gill,
  • Amjad M. Husaini

摘要

Fragrant rice, renowned for its superior grain characteristics and distinct aroma, commands a premium price in Indian and international markets. Aromatic rice genotypes have been shown to harbour a truncated version of the Betaine aldehyde dehydrogenase 2 (badh2) gene located on chromosome 8, which is responsible for fragrance production. In this study, we assessed Kashmir Himalayan rice genotypes (Mushk Budji, Jehlum and Kawa Kreed) and aromatic long-slender grain rice Pusa Sugandh-3 for allelic variations in exon 2 of the badh2 gene. Primers targeting exon 2 were designed based on previous research and successfully amplified a 200–207 bp fragment across the genotypes. The analysis revealed the presence of a 7-bp deletion (“CGGGCGC”), a 2-bp deletion (“AA”), and two single nucleotide polymorphisms (“CC”) in the badh2 exon 2 of the aromatic Mushk Budji genotype and 7-bp deletion (“CGGGCGC”) along with four single nucleotide polymorphisms (C, G, T, G → G, A, G, C) in Pusa Sugandh-3. This is the first report of these specific deletions and SNPs in these genotypes. Additionally, the ALU-I functional marker was used to confirm these variations, revealing distinct restriction patterns in aromatic cultivars, with cleaved fragments (158 bp and 322 bp) in Mushk Budji and Pusa Sugandh-3, and an intact 480 bp fragment in non-aromatic cultivars. No such variations were observed in non-aromatic rice cultivars. These findings provide valuable insights into the genetic basis of aroma in rice genotypes and could be utilised for crop improvement programs targeting aromatic rice traits.