Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm

Singh, G and Krishnan, S G and Kumar, A and Vinod, K K and Bollinedi, H and Ellur, R K and Nagarajan, M and Bhowmick, P K and Madhav, S M and Singh, K and Singh, A K (2022) Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm. Physiology and Molecular Biology of Plants (TSI), 28. pp. 1013-1027. ISSN 0971-5894

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Allelic variability of the aroma gene, betaine aldehyde dehydrogenase 2 (BADH2) was studied in a random subset of indigenous aromatic rice germplasm along with a few exotic aromatic accessions. Use of functional markers of four badh2 alleles identified that the test panel possessed only two alleles, badh2-E7 and badh2-p-5′UTR. Two other alleles, badh2.2 and badh2-E4-5.2 were absent. Based on the alleles present, four functional polymorphisms (FP) were detected, namely FP1 to FP4. 188 genotypes possessed FP1 having both the badh2-p-5′UTR and badh2-E7 (71.8%) alleles. The badh2 allele with FP1 is named badh2-E7-p. 39 genotypes (14.9%) possessed only the badh2-p-5′UTR allele (FP3), while three genotypes were found to carry only the badh2-E7 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 badh2-p1, 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 BADH2 characterization carried out in this study is suggestive of identifying the additional gene(s)/ allele(s) governing aroma among the Indian fragrant rice.

Item Type: Article
Divisions: Genebank
Uncontrolled Keywords: Grain aroma, 2-Acetyl-1-pyrroline, Betaine aldehyde dehydrogenase 2, badh2-E7-p, badh2-p-5′UTR, Quantitative analysis
Subjects: Others > Rice
Depositing User: Mr Nagaraju T
Date Deposited: 18 Mar 2024 04:17
Last Modified: 18 Mar 2024 04:17
Official URL:
Acknowledgement: Author’s wish to acknowledge the support rendered by the staff of Division of Genetics, IARI for conduct of experiments, and ICAR-Indian Institute of Rice Research, Hyderabad for the supply of seed materials for the germplasm panel used. This work is a part of the doctoral research of the senior author.
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