Badh2 gene-based DNA hybridization assay for non-fragrant and fragrant Thai rice detection

Abstract

2-Acetyl-1-pyrroline (2AP) is the major compound mixed in the aroma intensities of fragrant rice cultivars. The recessive gene betaine aldehyde dehydrogenase (badh2) controls the biosynthesis of 2AP in fragrant rice cultivars. However, the 2AP content was also found in non-fragrant rice cultivars based on the environmental factors of the cultivation areas. In this study, we developed a new allele-specific method (sandwich DNA hybridization assay) for the recessive badh2 gene assay to classify the non-fragrant and fragrant of Thai rice cultivars. Moreover, the 2AP content of all rice cultivars was investigated by the GC-MS method to confirm the specific distinction of this assay. The results showed that the 2AP content was determined in all rice cultivars with a range of 4.4 ± 0.06–323.0 ± 4.04 µg/g. The 2AP content of all rice cultivars could be categorized into two groups: the first group with a range of 4.4 ± 0.06–10.3 ± 0.26 µg/g, and the second group with a range of 101.7 ± 2.00–323.0 ± 4.04 µg/g. The DNA hybridization assay results indicated that the first group was comprised of non-fragrant rice cultivars, and the second group was comprised of fragrant rice cultivars. Thus, results further suggested that the newly developed method using a DNA hybridization assay confirmed the 2AP content of the non-fragrant and fragrant rice cultivars with the advantages of accuracy and selectivity. The proposed novel assay also was a suitable method for separating the non-fragrant rice cultivars from the fragrant rice cultivars.