Molecular profiling of locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm.

UNLABELLED

Allelic variability of the aroma gene, () was studied in a random subset of indigenous aromatic rice germplasm along with a few exotic aromatic accessions. Use of functional markers of four alleles identified that the test panel possessed only two alleles, and '. Two other alleles, and were absent. Based on the alleles present, four functional polymorphisms (FP) were detected, namely FP1 to FP4. 188 genotypes possessed FP1 having both the ' and (71.8%) alleles. The allele with FP1 is named . 39 genotypes (14.9%) possessed only the ' allele (FP3), while three genotypes were found to carry only the allele (FP2). We also found that 32 genotypes (12.2%) did not have any of the target aroma alleles tested in this study (FP4). Interestingly, for badh2-p-5'UTR marker, the expected 198 bp amplicon for the non-aromatic allele could not be detected among any of the genotypes tested. Instead, an amplicon of 456 bp length appeared with 100% presence in the non-aromatic checks. Notwithstanding, the 456 bp allele also showed a 16% presence among the aromatic lines. This article forms the first report of this allele, named , among aromatic rice. Quantification of 2-Acetyl-1-Pyrroline (2AP) content and sensory evaluation among the test genotypes showed that those with FP1 are highly aromatic than the genotypes carrying other types of FPs. But, a few strongly aromatic lines showed lower 2AP content. The characterization carried out in this study is suggestive of identifying the additional gene(s)/ allele(s) governing aroma among the Indian fragrant rice.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01181-9.