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.