Development And Utilization Of Markers Tagged To The Fragrant Gene In Rice

Fragrance is one of the important quality traits in rice. Among the 100 volatile flavor components, 2-acetyl-1-pyrroline (2AP) has proved to be a potent flavor one in rice fragrance. It has been reported that a recessive fgr gene on chromosome 8 is responsible for this fragrant trait. In our previous study, we delimited the gene responsible for fragrance between the molecular markers L02 and L06. There are three predicted genes within the interval of L02/L06, encoding respective eukaryotic-type carbonic anhydrase (CAH), 3-methylcrotonyl-CoA carboxylase beta chain (MCCC2), and betaine aldehyde dehydrogenase (BADH2). All three candidate genes have been cloned from both the fragrant rice cv.'Suyunuo'and the non-fragrant rice cv.'Nanjing11'BAC libraries. Sequence analysis between the fragrant and non-fragrant rice varieties revealed polymorphisms at three sites in the Badh2 coding region. Out of them, an 8-bp deletion and 3 SNPs in exon 7 would cause an immediate stop codon, resulting in a truncated BADH2 protein in fragrant genotypes. A pair of primers, designed on the flanking regions of this polymorphic site, was utilized to detect the fgr alleles for the 24 fragrant and 10 non-fragrant rice varieties. Within the 24 fragrant rice varieties, the mutant exon 7 could only be found in some fragrant varieties, for the remaining fragrant varieties, the exon 7 is the exactly same as that of the non-fragrant ones. Therefore, the fragrant varieties'Wuxiangjing9'and'Xiangjing111'with the intact exon 7 were used to sequence their whole fgr genes. Interestingly, a new mutant point in exon 1 with a 7-bp deletion was found. Accordingly, a new pair of primers was designed on the flanking region of this mutant point of the exon 1. After sequencing of 24 fragrant and 10 non-fragrant varieties in their exon 1, we found those fragrant varieties with intact exon 7 all showed the mutant exon 1 with a 7-bp deletion, and all the non-fragrant rice varieties had both intact exon 1 and 7.As a consequence, two fgr alleles are present in the fragrant rice varieties. The two markers we developed could distinguish fragrant from non-fragrant rice varieties as well as those different fragrant rice varieties, and would find their usefulness in identifying homozygous fragrant, homozygous non-fragrant, and heterozygous genotypes in the segregating population for fragrance.