Genetic Characterization of BADH2 in Philippine Aromatic Rice Cultivars

Fragrance is considered one of the most highly valued grain quality traits in rice, yet its genetic basis among Philippine cultivars, especially traditional accessions, is unknown. This study characterized the fragrance gene Betaine aldehyde dehydrogenase isoform 2 (BADH2) in selected Philippine aromatic rice cultivars at the DNA, transcript, and phenotypic level. DNA fragment length analysis showed that eight out of 18 cultivars were positive for badh2.1, an allele responsible for the accumulation of 2-acetyl-1-pyrroline (2AP), the marker compound for fragrance in rice. DNA sequence alignment of nine cultivars confirmed the absence of 8 base pairs (bp) and three single nucleotide polymorphism (SNPs) in exon 7 in Dinorado White, Saigorot, and Salanay, while revealing several other nucleotide variations in other coding regions and immediate upstream region of the gene. The BADH2 gene expression profile showed that aromatic cultivars have varying lower amounts of the BADH2 mRNA than the non-aromatic cultivars. Results in 2AP analysis showed significant discrepancies in 2AP levels among cultivars during wet and dry season, which may be due to some possible factors such as sequence variation in the coding regions of BADH2, affecting gene expression, and environmental factors such as exposure to stress or postharvest processes. Overall, results have shown that aroma production among the Philippine aromatic cultivars was not due to just one genetic mechanism. Further investigation regarding analysis at the protein level, characterization of regulatory mechanisms in gene expression, and finding new genes that may be involved in the production of aroma must be pursued.