Haplotype variation of Badh2 gene, unearthing of a new fragrance allele and marker development for non-basmati fragrant rice ‘Velchi’ (Oryza sativa L.)

In the present study, selected indica rice accessions (basmati, non-basmati fragrant, and non-fragrant) were screened for mutations in betaine aldehyde dehydrogenase 2 (badh2) gene to investigate the allelic differences using previously reported functional markers. This screening experiment revealed that non-basmati fragrant accession ‘Velchi’ does not harbour any reported mutation in coding region of badh2. While working with badh2-p-UTR marker we got deviating results. All the non-basmati fragrant and basmati types gave amplicon of 203 bp except Velchi, whereas all non-fragrant and ‘Velchi’ gave 456 and 461 bp amplicons respectively. The new allele has 253 bp deletion in the promoter region of fragrant indica rice accessions compared to non-fragrant rice. Further, the fragrant accession ‘Velchi’ has additional 5 bp duplication as compared to non-fragrant accessions. To distinguish Velchi from other non-fragrant indica accessions, a new marker (velbadh2-p-UTR) has been designed to identify this 5 bp difference, which could distinguish ‘Velchi’ from non-fragrant rice accessions and can be useful in breeding for development of fragrant rice varieties via marker-assisted selection. The 2AP biosynthesis related metabolites, gene expression and enzyme assay confirmed deletion in badh2 and expression of fragrance in Velchi.