Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.)
Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.)
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DOI：
10.1007/s11434-007-0472-x
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发表时间：
2007-11-01
影响因子：
--
通讯作者：
Shu Qingyao
中科院分区：
文献类型：
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作者：
Wang Caixia;Shu Qingyao
紫稻是一种在籽粒果皮中含有花青素的水稻品种。控制水稻紫皮性状的Pb基因位于第4染色体上，且紫色对白色显性。本研究利用培矮64 S（白色）×云南黑鲜糯（紫色）和培矮64 S ×川黑糯（紫色）两个F-2分离群体对Pb基因进行了精细定位。在第一遍定位中，Pb基因位于SSR标记RM 3820的下游区域。在精细定位中，候选区域被专门为本研究开发的InDel和CAPS标记饱和。最终，Pb基因定位在由上游标记RID 3和下游标记RID 4限定的25-kb区域内。划定的区域含有两个注释的基因Ra和bhlh 16（TIGR Rice Genome，R.5）。前者是玉米中控制花色素苷生物合成的Myc转录因子Lc的同源物，后者是拟南芥中控制果皮色素沉着的Myc转录因子基因TT 8的同源物。序列分析表明，云南黑籼糯和川黑糯的Ra基因第7外显子与白色水稻品种培矮64 S、9311和日本晴的Ra基因第7外显子相比有2个碱基的GT缺失。根据GT缺失的特点，设计了一个CAPS标记CAPSRa，用于对两个F-2分离群体和106个水稻品系的分析。结果表明，所有白色果皮的F-2代植株和所有非紫稻株系（63个白色和22个红色）均未检测到GT缺失，而20个紫稻株系均检测到GT缺失。这些结果表明，Ra基因可能是Pb基因，水稻紫皮特性是由Ra基因第7外显子GT缺失引起的。
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 F-2 segregating populations, i.e. Pei'ai 64S (white) x Yunanheixiannuo (purple) and Pei'ai 64S x 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 F-2 segregating populations and 106 rice lines. The results showed that all F-2 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.