Development of Two Functional Markers of <i>Badh2</i> Gene in Guangxi Fragrant Rice

Abstract

Fragrance in rice is one of the most important quality traits, which resulted from the loss of function of betaine aldehyde dehydrogenase ( Badh2 ) gene on chromosome 8. The mutation of  Badh2  leads to accumulation of 2-acetyl-1-pyrroline (2-AP), which is known as the main volatile in fragrant rice. At least 18 allelic variations have been identified in  Badh2  genes in rice. Marker assisted selection has proved to be an effective way of fragrant rice breeding. Traditional marker detection methods, such as Sanger sequencing or SSR molecular marker, are found to be low efficient. To develop a more dynamic method, we adopt Real-time PCR method to detect the common mutation site in Guangxi. In this study,  Badh2  gene of 40 fragrant rice accessions collected from Guangxi province was sequenced. Most of the fragrant rice accessions belonged to 806 bp deletion between exon 4-5 ( badh2-E4-5.1 ) and 8 bp deletion in exon 7 ( badh2-E7 ). Two Real-time PCR SNP molecular markers were developed, and were used to verify the 40 sequenced fragrant rice accessions. 93.75% of the detection results using Real-time PCR were consistent with the results of Sanger sequencing. Further, 50 local varieties were examined by Real-time PCR. A total of 24 accessions carry  badh-E4-5  allele and 22 accessions detected with  badh-E7 . The two functional SNP molecular markers common in Guangxi fragrant rice were developed and proved to be useful in rice breeding. These functional markers will improve the efficiency of fragrant rice breeding.