Allelic Variation and Haplotype Diversity of the badh2 Gene in Thai Aromatic Landrace Rice Varieties

Thai aromatic landrace rice varieties are vital reservoirs of genetic diversity for fragrance traits, offering valuable potential for rice breeding. This study characterized grain morphology, aroma, and the badh2 gene variation in aromatic and non-aromatic rice varieties.  Most aromatic varieties featured slender grains, typically with white pericarps. Sensory evaluation revealed varying aroma intensities across the panel. Badh2 gene sequences were analyzed for 14 allelic variations across introns and exons. Six exonic variations defined 4 haplotypes. Haplotype 1, including KDML105 and 17 others, shared an 8-bp deletion in exon 7. Haplotype 2, found only in Hawm Hua Bawm, had the same alleles as Haplotype 1 but a unique SNP (G > A) in exon 13, a novel allele associated with aroma expression. Haplotype 3 consisted of 8 varieties, lacking the 8-bp deletion in exon 7 and carrying the new allele in exon 13. Haplotype 4 was found in Hawm Gra Dang Ngah 59. All the alleles resembled non-aromatic rice, suggesting that aroma may result from functional mutations elsewhere in the badh2 gene or be influenced by different genes. Predicted functional impacts of exonic variants support the role of badh2 gene diversity in shaping aroma. These findings enhance our understanding of aroma genetics in rice and provide useful markers for breeding fragrant cultivars. HIGHLIGHTS The complete coding sequence of the fragrant gene (badh2) was characterized for haplotype diversity in 24 Thai aromatic rice landraces and three improved aromatic rice varieties. Fourteen allelic variations were detected in the badh2 gene, with four haplotypes identified using six alleles in the exon regions of the aromatic varieties. A new functional allele, SNP (G>A), was detected in exon 13 of the badh2 GRAPHICAL ABSTRACT