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Open Access Research article

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

Zehong Ding1, Chongrong Wang1, Sheng Chen2 and Sibin Yu1*

Author Affiliations

1 National Key Laboratory of Crop Genetic Improvement, and the College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China

2 School of Plant Biology, and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA 6009, Australia

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BMC Evolutionary Biology 2011, 11:61  doi:10.1186/1471-2148-11-61

Published: 8 March 2011

Additional files

Additional file 1:

Table S1: Details of sources, classification, and haplotypes of accessions of cultivated rice and wild rice used in this study.

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Additional file 2:

Table S2: Primers used for PCR amplification and sequencing. The targeted genes with positions relative to OsAMT1;1, annealing temperature, and predicted product size for amplification are listed.

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Additional file 3:

Table S3: Ka/Ks test for OsAMT1;1. Ka, Ks represent non-synonymous and synonymous substitutions rate respectively.

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Additional file 4:

Table S4: Summary of 21 annotated genes surrounding OsAMT1;1.

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Additional file 5:

Figure S1: Comparison of nucleotide diversity in OsAMT1;1 and two other genes related to nitrogen metabolism in O. rufipogon, landraces, and elite rice. (n) = no. of the samples assayed in each subgroup.

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Additional file 6:

Figure S2: Expression of OsAMT1;1 in paired near-isogenic lines under low nitrogen. NIL1 and NIL2 represent that near-isogenic line carried the OsAMT1;1 allele from 'ACC10' (O. rufipogon) and from 'Nipponbare' (japonica), respectively within the same genetic background of 'Zhenshan97' (ZS97). Young seedlings at the two-leaf stage were transferred to a Yoshida nutrient solution with one modification representing low nitrogen (0.15 mM (NH4)2SO4). The nutrient solution was replaced every three days. Seedlings were grown in the nutrient solution for seven days, after which their roots and shoots were harvested separately, frozen in liquid nitrogen, and stored at -70°C until required for RNA isolation. Total RNA was isolated using Trizol reagent (Invitrogen). qRT-PCR (quantitative real-time PCR) was performed using the forward primer 5'-CTGGGGTTGGTGGGTTCA-3' and reverse primer 5'-CACTTGGTTGTTGCTGTTGGAG-3' for OsAMT1;1 and the primers 5'-AACCAGCTGAGGCCCAAGA-3' and 5'-ACGATTGATTTAACCAGTCCATGA-3' for rice ubiquitin gene, which served as the internal control. Relative expression values are given as means ± standard error from three biological replications each with three technical repeats, and the p value next to each bar represents the results of t test between a given NIL and ZS97. Error bars indicate standard error.

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