水稻的单核苷酸多态性研究
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摘要
单核苷酸多态性(Single Nucleotide Polymorphisms，SNPs)是生物基因组中分布最丰富并能代表遗传变异背景的一种遗传变异类型。了解粳稻和籼稻的SNPs频率和单倍型的基因多样性，可以进一步在分子水平上阐明粳稻和籼稻遗传结构的差异。
本研究在水稻基因组12条染色体的两臂上各随机选择一个基因位点，共24个基因位点。在38个水稻(Oryza sativa L．)品种中均测定并获得清晰的DNA序列18989bp，共发现92个SNPs位点和70个单倍型。在92个SNPs中，65个(70.6％)SNPs为转换，转换为主要的置换方式。应用卡方同一性检验发现，在92个SNPs中有65个(70.6％)SNPs的等位基因频率在籼稻和粳稻间有显著性差异，其中5个基因位点上的11个SNPs能够准确辨别粳稻和籼稻。水稻SNPs分布不均，存在SNPs富集和SNPs贫乏的区域。粳稻和籼稻分别拥有32和67个SNPs，SNPs频率e值分别为0.47、1.02 SNPs／kb，SNPs频率π值分别为0.31×10~(-3)、1.27×10~(-3)。粳稻和籼稻分别有38和47种单倍型，籼稻和粳稻共同拥有15种单倍型。粳稻和籼稻的单倍型基因多样性均值分别为0.14、0.234。单倍型的分化系数(Gst)在0～1之间，不同基因位点单倍型的分化系数既有相同，也有不同。
从以上结果可看出：总体上，粳稻的遗传多样性低于籼稻的遗传多样性，粳稻和籼稻的分化显著。但在不同基因位点的籼粳分化程度既有相同，也有不同，表现出水稻群体结构的复杂性。此外，通过UPGMA聚类和Bayesian聚类可以清楚的区分粳稻和籼稻，而Bayesian聚类清楚的观察到水稻内存在的群体结构并辨别水稻品种的混合程度。Bayesian聚类将为水稻群体结构的解析和选择育种品种提供帮助。
Single Nucleotide Polymorphisms (SNPs) is a kind of genetic variation which is the most abundant variation in biological genome and can represent genetic background in truth. Through SNPs frequencies, allele frequencies at SNPs loci, gene frequancies and differentiation at SNPs loci, gene frequancies and differentiation at genome loci, we can clarify the genetic difference between japanica and indica at the DNA level.
DNA fragments in 24 loci distributed in each chromosome (18989 bp) were sequenced in the 38 accessions of Chinese Cultivated Rice (Oryza sativa L.) including 20 accessions of japonica and 18 accessions of indica. There were 92 SNPs and 75 haplotype in total. Of 92 SNPs, transitions accounted for 65 (70.6%). Allele frequencies at 65 (70.6%) SNPs loci showed significiant difference between japonica and indica. 11 SNPs at 5 genomic loci can distinguish japonica from indica. 32 and 67 SNPs were found respectively in japonica and indica. The SNPs frequency θ was 0.47, 1.02 SNPs/kb respectively in japonica and indica, and the SNPs frequency π was 0.31×10~(-3), 1.27×10~(-3) respectively. Mean differentiation of SNPs at intron region and exon region was lager than the mean differentiation of SNPs at intergene region. 38 and 47 haplotypes were detected in japonica and indica, and 15 common haplotypes. Mean haplotype divergence was 0.14, 0.234 in japonica and indica respectively. Haplotype differentiation (Gst) was beween 0 and 1.
From the result above, genetic divergence of japonica was lager than indica. The genetic differentiation between indica and japonica was significant. It showed the complexity of population structure in rice. Furthermore, UPGMA and Bayesian cluster can distinguish indica from japonica. Bayesian cluster can resolve population structure more clearly and observe the admixture of rice effectively.
本研究在水稻基因组12条染色体的两臂上各随机选择一个基因位点，共24个基因位点。在38个水稻(Oryza sativa L．)品种中均测定并获得清晰的DNA序列18989bp，共发现92个SNPs位点和70个单倍型。在92个SNPs中，65个(70.6％)SNPs为转换，转换为主要的置换方式。应用卡方同一性检验发现，在92个SNPs中有65个(70.6％)SNPs的等位基因频率在籼稻和粳稻间有显著性差异，其中5个基因位点上的11个SNPs能够准确辨别粳稻和籼稻。水稻SNPs分布不均，存在SNPs富集和SNPs贫乏的区域。粳稻和籼稻分别拥有32和67个SNPs，SNPs频率e值分别为0.47、1.02 SNPs／kb，SNPs频率π值分别为0.31×10~(-3)、1.27×10~(-3)。粳稻和籼稻分别有38和47种单倍型，籼稻和粳稻共同拥有15种单倍型。粳稻和籼稻的单倍型基因多样性均值分别为0.14、0.234。单倍型的分化系数(Gst)在0～1之间，不同基因位点单倍型的分化系数既有相同，也有不同。
从以上结果可看出：总体上，粳稻的遗传多样性低于籼稻的遗传多样性，粳稻和籼稻的分化显著。但在不同基因位点的籼粳分化程度既有相同，也有不同，表现出水稻群体结构的复杂性。此外，通过UPGMA聚类和Bayesian聚类可以清楚的区分粳稻和籼稻，而Bayesian聚类清楚的观察到水稻内存在的群体结构并辨别水稻品种的混合程度。Bayesian聚类将为水稻群体结构的解析和选择育种品种提供帮助。
Single Nucleotide Polymorphisms (SNPs) is a kind of genetic variation which is the most abundant variation in biological genome and can represent genetic background in truth. Through SNPs frequencies, allele frequencies at SNPs loci, gene frequancies and differentiation at SNPs loci, gene frequancies and differentiation at genome loci, we can clarify the genetic difference between japanica and indica at the DNA level.
DNA fragments in 24 loci distributed in each chromosome (18989 bp) were sequenced in the 38 accessions of Chinese Cultivated Rice (Oryza sativa L.) including 20 accessions of japonica and 18 accessions of indica. There were 92 SNPs and 75 haplotype in total. Of 92 SNPs, transitions accounted for 65 (70.6%). Allele frequencies at 65 (70.6%) SNPs loci showed significiant difference between japonica and indica. 11 SNPs at 5 genomic loci can distinguish japonica from indica. 32 and 67 SNPs were found respectively in japonica and indica. The SNPs frequency θ was 0.47, 1.02 SNPs/kb respectively in japonica and indica, and the SNPs frequency π was 0.31×10~(-3), 1.27×10~(-3) respectively. Mean differentiation of SNPs at intron region and exon region was lager than the mean differentiation of SNPs at intergene region. 38 and 47 haplotypes were detected in japonica and indica, and 15 common haplotypes. Mean haplotype divergence was 0.14, 0.234 in japonica and indica respectively. Haplotype differentiation (Gst) was beween 0 and 1.
From the result above, genetic divergence of japonica was lager than indica. The genetic differentiation between indica and japonica was significant. It showed the complexity of population structure in rice. Furthermore, UPGMA and Bayesian cluster can distinguish indica from japonica. Bayesian cluster can resolve population structure more clearly and observe the admixture of rice effectively.
引文
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