Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.)
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Purple rice is a type of rice with anthocyanins deposited in its grain pericarp. The rice Pb gene controlling purple pericarp character is known to be on chromosome 4, and the purple color is dominant over white color. In this study, we fine mapped the Pb gene using two F2 segregating populations, i.e. Pei’ai 64S (white) × Yunanheixiannuo (purple) and Pei’ai 64S × Chuanheinuo (purple). In the first-pass mapping, the Pb gene was located in the region downstream the SSR marker RM3820. In the fine mapping, the candidate region was saturated with InDel and CAPS markers developed specifically for this study. Eventually, the Pb gene was mapped within the 25-kb region delimited by the upstream marker RID3 and the downstream marker RID4. The delimited region contained two annotated genes, Ra and bhlh16 (TIGR Rice Genome, R.5). The former is a homologue of the Myc transcription factor Lc controlling anthocyanin biosynthesis in maize, and the latter is a homologue of the TT8 gene, which is also an Myc transcription factor gene controlling the pericarp pigmentation in Arabidopsis thaliana. Sequence analysis showed that the exon 7 of the Ra gene of Yunanheixiannuo and Chuanheinuo had a 2-bp (GT) deletion compared with those of the white rice varieties Pei’ai 64S, 9311 and Nipponbare. A CAPS marker, CAPSRa, was developed according to the GT deletion for analysis of the two F2 segregating populations and 106 rice lines. The results showed that all F2 plants with white pericarp, and all non-purple rice lines (63 white and 22 red) contained no GT deletion, but all 20 purple rice lines contained the GT deletion. These results suggested that the Ra gene may be the Pb gene and the purple pericarp characteristic of rice is caused by the GT deletion within exon 7 of the Ra gene.
KeywordsOryza sativa purple pericarp Pb gene fine mapping Ra gene
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- 3.Nagao S, Takahashi M. Genetical studies on rice plants. XXVII. Trial construction of twelve linkage groups in Japanese rice. J Fac Agri Hokkaido Univ, 1963, 53: 72–130Google Scholar
- 4.Causse M A, Fulton T M, Cho Y G, et al. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics, 1994, 138: 1251–1274Google Scholar
- 6.Hu J P, Anderson B, Wessler S R. Isolation and characterization of rice R genes: Evidence for distinct evolutionary paths in rice and maize. Genetics, 1996, 142: 1021–1031Google Scholar
- 9.Zhuang J Y, Yang C D, Qian H R, et al. Linkage analysis of RFLP markers and the gene for purple pericarp of rice (in chinese). Acta Genetica Sinica, 1996, 23(5): 372–375Google Scholar
- 10.Lu Y J, Zheng K L. A convenient method for isolating genomic DNA from rice (in chinese). Chin J Rice Sci, 1992, 6: 47–48Google Scholar
- 14.Ludwig S R, Habera L F, Dellaporta S L, et al. Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proc Natl Acad Sci USA, 1989, 86: 7092–7096CrossRefGoogle Scholar
- 18.Zhao C Z, Qi X F, Yang C D et al. Study of ‘Black superior rice’ selected by the use of somaclonal variation (in chinese). J Agri Biotech, 1993, 1(1): 100–105Google Scholar