野生稻Oryza nivara和O. rufipogon DNA甲基化多样性

doi:10.3724/SP.J.1003.2010.227

摘要/Abstract

摘要：

本文调查研究了野生稻群体内及群体间的DNA甲基化多样性。选取与亚洲栽培稻近缘的两个野生种Oryza nivara和O. rufipogon作为研究对象, 采用改进的MSAP (methylation-sensitive amplification polymorphism)技术对其基因组CCGG位点的甲基化多样性进行了分析。结果表明: 在同一个IRGC(the International Rice Germplasm Center)编号群体内的不同个体间, 基因组甲基化条带高度一致; 而在不同编号群体间, 甲基化条带表现为多态。其中后者又可以分为两类: 条带模式高度一致的Class I和条带模式呈多态性的Class II。将上述两类甲基化片段的编码基因与栽培稻粳稻(O. sativaL. subsp. japonica)和籼稻(O. sativa L. subsp. indica)两个亚种的同源基因进行序列比对发现, 在进化趋势上Class I表现得比较保守, 而Class II较为活跃。DNA甲基化多样性作为标志遗传多样性的一种信息来源, 其在群体分化及物种进化过程中的作用还需要进一步探讨。

关键词: 表观等位基因, MSAP, 群体分化, 进化

Abstract

Intra- and inter-population methylation diversity at CCGG sites were surveyed in the genomes of Oryza nivaraandO. rufipogonusing a modified MSAP (methylation-sensitive amplification polymorphism) technique. These two wild species were closely related to cultivated rice in that they share the common A genome. Results revealed that methylated bands were uniform among different individuals of the same IRGC (International Rice Germplasm Center) accession, but polymorphic among different populations within the IRGC. Methylated bands could be divided into two categories, i.e., the conserved group (Class I), and the polymorphic group (Class II). Comparing the gene sequences of the two classes to the homologous sequences of japonica and indica varieties, Class I was conservative, but Class II was variable and evolutionarily active. DNA methylation diversity was an informative indicator of genetic diversity in Oryza. However, further studies of population differentiation and species evolution are needed.

Key words: epialleles, MSAP, population differentiation, evolution

崔影影, 张大明 (2010) 野生稻Oryza nivara和O. rufipogon DNA甲基化多样性. 生物多样性, 18, 227-232. DOI: 10.3724/SP.J.1003.2010.227.

Yingying Cui, Daming Zhang (2010) Surveying DNA methylation diversity in the wild rice, Oryza nivaraand O. rufipogon. Biodiversity Science, 18, 227-232. DOI: 10.3724/SP.J.1003.2010.227.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2010.227

https://www.biodiversity-science.net/CN/Y2010/V18/I3/227

图/表 5

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序号 Index	IRGC编号 IRGC No.	来源地 Geographic origin
O. nivara
N1	103407	斯里兰卡 Sri LanKa
N2	105431	斯里兰卡 Sri LanKa
N3	105391	泰国 Thailand
N4	106345	缅甸 Myanmar
N5	106185	印度 India
O. rufipogon
R1	106515	越南 Vietnam
R2	82000	巴布亚新几内亚 Papua New Guinea
R3	103423	斯里兰卡 Sri LanKa
R4	105958	印度尼西亚 Indonesia
R5	106036	马来西亚 Malaysia

序号 Index	IRGC编号 IRGC No.	来源地 Geographic origin
O. nivara
N1	103407	斯里兰卡 Sri LanKa
N2	105431	斯里兰卡 Sri LanKa
N3	105391	泰国 Thailand
N4	106345	缅甸 Myanmar
N5	106185	印度 India
O. rufipogon
R1	106515	越南 Vietnam
R2	82000	巴布亚新几内亚 Papua New Guinea
R3	103423	斯里兰卡 Sri LanKa
R4	105958	印度尼西亚 Indonesia
R5	106036	马来西亚 Malaysia

引物与接头 Primer and adapter	序列(5′-3′) Sequence(5′-3′)
接头 Adapter
EcoRI-adapter I	CTGGTAGACTGCGTACC
EcoRI-adapter II	AATTGGTACGCAGTC
预扩增引物 Preselective primer
EcoRI + A	GACTGCGTACCAATTCA
EcoRI + C	GACTGCGTACCAATTCC
选择性扩增引物 Selective primer
EcoRI + AA	GACTGCGTACCAATTCAA
EcoRI + AT	GACTGCGTACCAATTCAT
EcoRI + AC	GACTGCGTACCAATTCAC
EcoRI + AG	GACTGCGTACCAATTCAG
EcoRI + CT	GACTGCGTACCAATTCCT
EcoRI + CG	GACTGCGTACCAATTCCG
EcoRI + CA	GACTGCGTACCAATTCCA

引物与接头 Primer and adapter	序列(5′-3′) Sequence(5′-3′)
接头 Adapter
EcoRI-adapter I	CTGGTAGACTGCGTACC
EcoRI-adapter II	AATTGGTACGCAGTC
预扩增引物 Preselective primer
EcoRI + A	GACTGCGTACCAATTCA
EcoRI + C	GACTGCGTACCAATTCC
选择性扩增引物 Selective primer
EcoRI + AA	GACTGCGTACCAATTCAA
EcoRI + AT	GACTGCGTACCAATTCAT
EcoRI + AC	GACTGCGTACCAATTCAC
EcoRI + AG	GACTGCGTACCAATTCAG
EcoRI + CT	GACTGCGTACCAATTCCT
EcoRI + CG	GACTGCGTACCAATTCCG
EcoRI + CA	GACTGCGTACCAATTCCA

种 Species	大小 Size (bp)	E值 E value	基因库 GenBank	染色体 Chromosome	检索结果 Result of BLAST
Class I
O. nivara	494	0	AP008217	11,12	Internal region of two genes; predicted as promoter region (0.9)
O. nivara	644	0	AP008217	11,12	Internal region of two genes; predicted as promoter region (0.9)
O. rufipogon	615	0	AP005531	8	RNA-binding region RNP-1containing protein (BAD05783)
	640	0	AP008218	11,12	Internal region of two genes; predicted as promoter region (0.85)
	548	0	AP008212	6	Putative mitochondrial phosphate transporter (BAD35704.1)
	282	6.00E-13	AC104322	3	Putative polyprotein (AAR89842.1)
Class II
O. nivara	742	0	AP008216.1	2,10	Internal region of two genes; predicted as promoter region (0.97/ 0.89)
	630	0	AP005563	9	TPR-like domain containing protein (BAD19882.1)
	218	4.00E-61	AL731583	4	Ribonuclease HI (CAE 05186.2)
O. rufipogon	366	0	AP008210	4	Kinesin, motor region domain containing protein (CAE04590.2)
O. rufipogon	563	7.00E-56	AP008213	7	Internal region of two genes; predicted as promoter region (0.99)
Class III
O. nivara	569	0	AC120529	3	Near the centromere, the internal region of putative protein and retrotransposon
	305	2.00E-11	AP008208.1	2	Inetrnal region of a pseudo gene
	681	0	AP008209	3	Snabo-1 miniature inverted repeat transposable element/ the intron of pseudo gene
	615	0	AC120529	3	Near the centromere, the internal region of putative protein and retrotransposon
O. rufipogon	478	0	AC120529	3	Near the centromere, the internal region of putative protein and retrotransposon
	599	0	AP004364.4	11,12	Internal region of two hypotetical protein
	514	0	AP008209.1	3	Near the centromere, the internal region of putative protein and retrotransposon