A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice



With 3 figures and 3 tables


Fragrance is an important quality trait of rice, which is mainly controlled by loss-function of the betaine aldehyde dehydrogenase gene (badh2) on rice chromosome 8. Two deletion mutations of Badh2 have been reported to associate with fragrance in rice. Allelic test showed that the fragrant gene of ‘Zaimiaoxiangnuo’ is allelic to badh2-E7 (8 bp deletion in exon 7 of Badh2). Sequencing and BLAST analysis showed that the allele in ‘Zaimiaoxiangnuo’ is a new mutation, i.e. deletion of 803 bp between exons 4 and 5. A marker FMbadh2-E4-5 was developed for the detection of the new deletion site of fragrant gene. FMbadh2-E4-5 and the two previously reported functional markers were used to genotype the fragrant genes of four non-fragrant and 22 fragrant rice varieties. The deletions were absent in all non-fragrant rice varieties, but present in all fragrant rice varieties. Eight fragrant rice varieties were positive for the FMbadh2-E4-5 marker. These findings are useful in the breeding of fragrant rice varieties.