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

BMC Evolutionary Biology

Research Article

Sibin Yu¹  Chongrong Wang¹  Zehong Ding¹  Sheng Chen² 

[1] National Key Laboratory of Crop Genetic Improvement, and the College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, 6009, Crawley, WA, Australia;

关键词: Nucleotide Diversity;    Single Nucleotide Polymorphism;    Wild Rice;    Artificial Selection;    Selective Sweep;   

DOI  :  10.1186/1471-2148-11-61

 received in 2010-09-28, accepted in 2011-03-08,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundAmmonium 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.ResultsNucleotide 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Ding et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.