Diversity and selective sweep in the OsAMT1;1 genomic region of rice.
Diversity and selective sweep in the OsAMT1;1 genomic region of rice.
复制标题
水稻 OsAMT1;1 基因组区域的多样性和选择性扫描
DOI：
10.1186/1471-2148-11-61
复制
发表时间：
2011-03-08
影响因子：
3.4
通讯作者：
Yu S
中科院分区：
文献类型：
--
作者：
Ding Z;Wang C;Chen S;Yu S
背景
铵态氮是植物生长所需氮素的主要形式之一。OsAMT 1;1是水稻（Oryza sativa L.）中的高亲和力铵转运蛋白，负责在低氮浓度下的铵吸收。该基因的表达模式已被报道。然而，其核苷酸的变异及其从野生祖先的进化途径尚未阐明。在这项研究中，OsAMT 1;1基因的核苷酸多样性和7个基因片段的多样性模式，跨越基因组区域约150 kb长的基因周围的基因进行了调查，通过测序的面板216个水稻种质，包括栽培稻和野生近缘种。
结果
OsAMT 1;1基因在栽培稻中的多态性（Pi）为0.00004，仅为普通野生稻的2.3%。rufipogon）。在O.燕麦。在所有材料中，在该基因的5'上游和3'下游延伸的整个区域中，中性测试值均为显著阴性。在O. sativa，但O.在OsAMT 1;1的启动子的任一侧上的rufipogon，证明了在铵转运蛋白内或附近的强自然选择。
结论
水稻OsAMT 1;1核苷酸变异的严重减少是由于OsAMT 1;1周围的选择性扫描造成的，这可能反映了水稻驯化过程中水稻土强选择下的氮素吸收系统。纯化选择也发生在野生稻分化成籼、粳两个亚种之前。这些发现将为水稻氮吸收基因的进化和驯化过程提供有益的见解。
Background
Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives.
Results
Nucleotide polymorphism (Pi) of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa), only 2.3% of that in the common wild rice (O. rufipogon). A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter.
Conclusions
The severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.
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