Research Report

Development of Two Functional Markers of Badh2 Gene in Guangxi Fragrant Rice  

Yu Zeng1 , Xinghai Yang2 , Xiuzhong Xia2 , Baoxuan Nong2 , Zongqiong Zhang2 , Zhijian Xu2 , Can Chen1 , Danting Li2
1 Guangxi Academy of Agricultural Science, Nanning, 530007, China
2 Guangxi Key Laboratory of Rice Research Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning, 530007, China
Author    Correspondence author
Rice Genomics and Genetics, 2022, Vol. 13, No. 5   doi: 10.5376/rgg.2022.13.0005
Received: 16 May, 2022    Accepted: 30 May, 2022    Published: 24 Jul., 2022
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This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Zeng Y., Yang X.H., Xia X.Z., Nong B.X., Zhang Z.Q., Xu Z.J., Chen C., Deng G.F., and Li D.T., 2022, Development of two functional markers of Badh2 gene in Guangxi fragrant rice, Rice Genomics and Genetics, 13(5): 1-6 (doi: 10.5376/rgg.2022.13.0005)


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.

Fragrant rice; Marker assisted selection; Fluorescence functional marker; Real-time PCR
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. Yu Zeng
. Xinghai Yang
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. Can Chen
. Danting Li
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