Surveying DNA methylation diversity in the wild rice, Oryza nivaraand O. rufipogon

doi:10.3724/SP.J.1003.2010.227

Abstract

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

Yingying Cui, Daming Zhang. Surveying DNA methylation diversity in the wild rice, Oryza nivaraand O. rufipogon[J]. Biodiv Sci, 2010, 18(3): 227-232.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2010.227

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

Figures/Tables 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