Dataset Information

Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

ABSTRACT:

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.

SUBMITTER: Ding Z

PROVIDER: S-EPMC3062601 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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Publications

Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

Ding Zehong Z Wang Chongrong C Chen Sheng S Yu Sibin S

BMC evolutionary biology 20110308

<h4>Background</h4>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 diversit ...[more]

PMID: 21385389

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Project description:BackgroundIt is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations. Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms, it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location. To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions.ResultsWe selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP) markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional (1)H-nuclear magnetic resonance (NMR). We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (r(s) = 0.14) by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm (1)H chemical shift) and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the (1)H chemical shift) against genetic distance matrices (derived from sets of 3 adjacent markers along each chromosome), generated clear correlations (r(s) > 0.4, p < 0.001) at 34 RFLP markers.ConclusionThis combinatorial approach will be valuable for exploring the correlative relationships between metabolic and genomic diversity. It will facilitate the elucidation of complex regulatory networks and those of evolutionary significance in plant metabolic systems.

Dataset Information

Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

Background

Results

Conclusions

Publications

Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

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