Discovery of a new fragrance allele and development of functional markers for identifying diverse fragrant genotypes in rice

作者：Shi, Yaqiong; Zhao, Guochao; Xu, Xiaolong; Li, Jianyue^*

来源：Molecular Breeding, 2014, 33(3): 701-708.

DOI：10.1007/s11032-013-9986-x

• Fragrant rice
• Discovery of a new fragrance allele
• badh2-p-5 ' UTR
• badh2-E2
• badh2-E7
• Development of functional markers

Discovery of new fragrance alleles provides important genetic resources for breeding fragrant rice. In this study, a hybrid complementation test demonstrated the association of a new fragrance allele without mutation in the coding region with flavor formation in a fragrant rice variety Nankai 138. The new allele (badh2-p-5'UTR) has a 3-bp deletion in the 5' untranslated region and an 8-bp insertion in the promoter (-1,314 site upstream from the initiation codon). Surprisingly, we found that there is also an 8-bp insertion in the promoter of the badh2-E7 allele. We developed a new sequence tagged site functional marker to identify the badh2-p-5'UTR and badh2-E7 alleles according to the 8-bp insertion in their promoters. A cleaved amplified polymorphic sequence (AluI) functional marker targeting a common base substitution in the intron 2 of three badh2 alleles, viz. badh2-p-5'UTR, badh2-E7 and badh2-E2, was developed to identify diverse genotypes for fragrance in rice. Based on the results of sequence alignments among the three badh2 alleles, we suggest that the badh2-E7 and badh2-p-5'UTR alleles may have the same genetic origin. In addition, the genetic distance between the badh2-E7 and badh2-p-5'UTR alleles may be closer than that between the badh2-E2 and the badh2-p-5'UTR alleles, or between the badh2-E2 and the badh2-E7 alleles.

• 出版日期2014-3
• 单位上海师范大学