Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.)
Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.)
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DOI：
10.1270/jsbbs.60.390
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发表时间：
2010-12-01
期刊：
影响因子：
2.4
通讯作者：
Yano, Masahiro
中科院分区：
文献类型：
--
作者：
Ebana, Kaworu;Yonemaru, Jun-ichi;Yano, Masahiro
为了揭示亚洲水稻（Oryza sativa L.）品种，我们调查了全基因组单核苷酸多态性（SNPs）在140个不同的加入。通过对水稻无名基因外显子和内含子的PCR扩增产物进行测序，共发现4357个SNP，分布在12条染色体上。我们检测到4.87个SNP/1 kb全基因组。通过对140份种质资源进行单核苷酸多态性分类，我们确定了7个品种群，反映了种质资源的地理分布。三个品种组被定义为热带粳稻，对应于以前的类别，和三个籼稻品种组也被定义在籼稻。SNPs之间的连锁不平衡（LD）的距离约为250 kb，除了一个较长的LD中检测到的Indica I品种组（对应于先前确定的aus组）。SNPs的等位基因频率在品种组之间存在差异，反映了各组的遗传多样性水平。这些SNPs的不同加入增强了我们对水稻自然变异的理解。
To reveal the sequence diversity and population structure of Asian rice (Oryza saliva L.) cultivars, we surveyed genome-wide single-nucleotide polymorphisms (SNPs) in 140 diverse accessions. We identified 4357 SNPs distributed on the 12 chromosomes by sequencing PCR amplicons from the exons and introns of anonymous rice genes. We detected 4.87 SNPs per 1 kb genome-wide. By classifying the 140 accessions on the basis of these SNPs, we identified seven cultivar groups that reflected the geographical distribution of the accessions. Three cultivar groups were defined from tropical japonica that corresponded to previous categories, and three indica cultivar groups were also defined within indica. The linkage disequilibrium (LD) distance between SNPs was approximately 250 kb, except for a longer LD detected in the Indica I cultivar group (corresponding to the previously identified aus group). The allele frequency of the SNPs varied among cultivar groups, reflecting the level of genetic diversity in each group. These SNPs for the diverse accessions enhance our understanding of natural variation in rice.