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<p>Fragrance is the most valued grain quality trait in rice, yet the genetic augmentation for high yield coupled with aroma is rarely achieved. Evolutionary relationship revealed that the <i>BADH2</i> gene was descended from dicot to monocot plants, more precisely to <i>Oryza</i> species, and then to other monocots during the course of evolution. However, while domestication the selection of fragrant plant types resulted in the sub-population of aromatic group of rice. In the present study, molecular characterization of Pusa Basmati-1 and Badshabhog (both aromatic) revealed the 260&#xa0;bp aromatic allele by the typical functional marker ‘FMbadh2-E7’, while Dudh Kandar showed a 268&#xa0;bp amplicon. Multiple sequence alignment based on sequence homology of <i>BADH2</i> gene in 98 accessions revealed the typical 8&#xa0;bp deletion (GATTATGG) in 7th exon of Pusa Basmati-1 and Badshabhog, but intact in the non-aromatic land race Dudh Kandar. Besides, the most typical SNPs were substitution mutation A/T and C/T before and after the 8&#xa0;bp deletion which distinguished aromatic and non-aromatic cultivars. Sequence variation in <i>BADH2</i> aroma gene displayed higher haplotype diversity (0.63749) compared to nucleotide diversity (0.005296) signifying evolution of divergent haplotypes among the populations. Haplotype analysis and clustering pattern based on sequence homology of the aroma gene showed distinct non-aromatic and aromatic groups due to their inherent typical sequence variation. Thus, <i>BADH2</i> locus-specific sequence variations may be useful for varietal identification, and as such, the functional marker (FMbadh2-E7) can be safely used for development of fragrant rice varieties through marker assisted breeding.</p>

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BADH2 gene-specific sequence variation and phylogenetic relationship in aromatic rice (Oryza sativa L.)

  • 期刊论文

  • 发表日期：

    2025年10月28日

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  • Swapan Kumar Tripathy,
  • Kundansing Rajpalsing Jadhao,
  • Jyoti Prakash Sahoo

摘要

Fragrance is the most valued grain quality trait in rice, yet the genetic augmentation for high yield coupled with aroma is rarely achieved. Evolutionary relationship revealed that the BADH2 gene was descended from dicot to monocot plants, more precisely to Oryza species, and then to other monocots during the course of evolution. However, while domestication the selection of fragrant plant types resulted in the sub-population of aromatic group of rice. In the present study, molecular characterization of Pusa Basmati-1 and Badshabhog (both aromatic) revealed the 260 bp aromatic allele by the typical functional marker ‘FMbadh2-E7’, while Dudh Kandar showed a 268 bp amplicon. Multiple sequence alignment based on sequence homology of BADH2 gene in 98 accessions revealed the typical 8 bp deletion (GATTATGG) in 7th exon of Pusa Basmati-1 and Badshabhog, but intact in the non-aromatic land race Dudh Kandar. Besides, the most typical SNPs were substitution mutation A/T and C/T before and after the 8 bp deletion which distinguished aromatic and non-aromatic cultivars. Sequence variation in BADH2 aroma gene displayed higher haplotype diversity (0.63749) compared to nucleotide diversity (0.005296) signifying evolution of divergent haplotypes among the populations. Haplotype analysis and clustering pattern based on sequence homology of the aroma gene showed distinct non-aromatic and aromatic groups due to their inherent typical sequence variation. Thus, BADH2 locus-specific sequence variations may be useful for varietal identification, and as such, the functional marker (FMbadh2-E7) can be safely used for development of fragrant rice varieties through marker assisted breeding.