Ma J, Bennetzen JL: Rapid recent growth and divergence of rice nuclear genomes. Proc Nati Acad Sci USA. 2004, 101: 12404-12410. 10.1073/pnas.0403715101.
Article
CAS
Google Scholar
Panaud CR: The molecular bases of cereal domestication and the history of rice. Biologies. 2009, 332: 267-272. 10.1016/j.crvi.2008.09.003.
Article
CAS
PubMed
Google Scholar
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch SR: Genetic structure and diversity in Oryza sativa L. Genetics. 2005, 169: 1631-1638. 10.1534/genetics.104.035642.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCouch SR, Sweeney M, Li JM, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao JH, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yuan LP, Ahn S: Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica. 2006, 154: 317-339. 10.1007/s10681-006-9210-8.
Article
Google Scholar
Tanksley SD, McCouch SR: Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 1997, 277: 1063-1066. 10.1126/science.277.5329.1063.
Article
CAS
PubMed
Google Scholar
Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD: Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS Genetics. 2007, 3 (9): 1745-1756. 10.1371/journal.pgen.0030163.
Article
CAS
PubMed
Google Scholar
Zhu QH, Zheng XM, Luo JC, Gaut BS, Ge S: Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol. 2007, 24 (3): 875-888. 10.1093/molbev/msm005.
Article
CAS
PubMed
Google Scholar
Li C, Zhou A, Sang T: Rice domestication by reducing shattering. Science. 2006, 311: 1936-1939. 10.1126/science.1123604.
Article
CAS
PubMed
Google Scholar
Sang T, Ge S: Genetics and phylogenetics of rice domestication. Current Opinion in Genetics and Development. 2007, 17: 533-538. 10.1016/j.gde.2007.09.005.
Article
CAS
PubMed
Google Scholar
Zhang LB, Zhu QH, Wu ZQ, Ibarra JR, Gaut BS, Ge S, Sang T: Selection on grain shattering genes and rates of rice domestication. New Phytologist. 2009, 184 (3): 708-720. 10.1111/j.1469-8137.2009.02984.x.
Article
CAS
PubMed
Google Scholar
Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD: Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics. 2006, 173: 975-983. 10.1534/genetics.106.056473.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR: Global dissemination of a single mutation conferring white pericarp in rice. PLOS Genet. 2007, 3 (8): 1418-1424. 10.1371/journal.pgen.0030133.
Article
CAS
Google Scholar
Wang RL, Stec A, Hey J, Lukens L, Doebley J: The limits of selection during maize domestication. Nature. 1999, 398: 236-239. 10.1038/18435.
Article
CAS
PubMed
Google Scholar
Doebley J, Stec A, Hubbard L: The evolution of apical dominance in maize. Natrue. 1997, 386: 485-488. 10.1038/386485a0.
Article
CAS
Google Scholar
Clark RM, Linton E, Messing J, Doebley JF: Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Nati Acad Sci USA. 2002, 101 (3): 700-707. 10.1073/pnas.2237049100.
Article
Google Scholar
Palaisa KA, Morgante M, Williams M, Rafalski A: Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. The Plant Cell. 2003, 15: 1795-1806. 10.1105/tpc.012526.
Article
CAS
PubMed
PubMed Central
Google Scholar
Palaisa K, Morgante M, Tingey S, Rafalski A: Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Nati Acad Sci USA. 2004, 101 (26): 9885-9890. 10.1073/pnas.0307839101.
Article
CAS
Google Scholar
Wang MY, Siddiqi MY, Ruth TJ, Glass ADM: Ammonium uptake by rice roots (II. Kinetics of 13NH4+ influx across the plasmalemma). Plant Physiology. 1993, 103 (4): 1259-1267. 10.1104/pp.103.4.1463.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kronzucker HJ, Glass ADM, Siddiqi MY: Kinetics of NH4+ influx in spruce. Plant Physiology. 1996, 110 (3): 773-779.
CAS
PubMed
PubMed Central
Google Scholar
Loque D, von Wiren N: Regulatory levels for the transport of ammonium in plant roots. Journal of Experimental Botany. 2004, 55 (401): 1293-1305. 10.1093/jxb/erh147.
Article
CAS
PubMed
Google Scholar
Li BZ, Mike M, Li SM, Li HY, Zhu SW, Shi WM, Su YH: Molecular basis and regulation of ammonium transporter in rice. Rice Science. 2009, 16 (4): 314-322. 10.1016/S1672-6308(08)60096-7.
Article
Google Scholar
Kaiser BN, Rawat SR, Siddiqi MY, Masle J, Glass AD: Functional analysis of an Arabidopsis T-DNA 'Knockout' of the high-affinity NH4+ transporter AtAMT1;1. Plant Physiology. 2002, 130: 1263-1275. 10.1104/pp.102.010843.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salvemini F, Marini AM, Riccio A, Patriarca EJ, Chiurazzi M: Functional characterization of an ammonium transporter gene from Lotus japonicus. Gene. 2001, 270: 237-243. 10.1016/S0378-1119(01)00470-X.
Article
CAS
PubMed
Google Scholar
Ludewig U, Wilken S, Wu B, Jost W, Obrdlik P, Ei Bakkoury M, Marini AM, Andre B, Hamacher T, Boles E, von Wiren N, Frommer WB: Homo- and hetero-oligomerization of ammonium transporter-1 NH4+ uniporters. The Journal of Biological Chemistry. 2003, 278 (46): 45603-45610. 10.1074/jbc.M307424200.
Article
CAS
PubMed
Google Scholar
Loque D, Yuan LX, Kojima S, Gojon A, Wirth J, Gazzarrini S, Ishiyama K, Takahashi H, von Wiren N: Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis root. The Plant Journal. 2006, 48: 522-534. 10.1111/j.1365-313X.2006.02887.x.
Article
CAS
PubMed
Google Scholar
Yuan LX, Loque D, Kojima S, Rauch S, Ishiyama K, Inoue E, Takahashi H, von Wiren N: The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial arrangement and biochemical properties of AMT1-type transporters. The Plant Cell. 2007, 19: 2636-2652. 10.1105/tpc.107.052134.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar A, Silim SN, Okamoto M, Siddiqi MY, Glass ADM: Differential expression of three members of the AMT1 gene family encoding putative high-affinity NH4+ transporters in roots of Oryza sativa subspecies indica. Plant, Cell and Environment. 2003, 26: 907-914. 10.1046/j.1365-3040.2003.01023.x.
Article
CAS
PubMed
Google Scholar
Sonoda Y, Ikeda A, Saiki S, von Wiren N, Yamaya T, Yamaguchi J: Distinct expression and function of three ammonium transporter genes (OsAMT1;1-1;3) in rice. Plant Cell Physiology. 2003, 44 (7): 726-734. 10.1093/pcp/pcg083.
Article
CAS
PubMed
Google Scholar
Sonoda Y, Ikeda A, Saiki S, Yamaya T, Yamaguchi J: Feedback regulation of the ammonium transporter gene family AMT1 by glutamine in rice. Plant Cell Physiology. 2003, 44 (12): 1396-1402. 10.1093/pcp/pcg169.
Article
CAS
PubMed
Google Scholar
Wen WW, Mei HW, Feng FJ, Yu SB, Huang ZC, Wu JH, Chen L, Xu XY, Luo LJ: Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet. 2009, 119: 459-470. 10.1007/s00122-009-1052-z.
Article
PubMed
Google Scholar
Rogers SO, Bendich AJ: Extraction of DNA from plant tissue. Plant Mol Biol Manual. 1988, A6: 1-10.
Google Scholar
Nei M: Molecular Evolutionary Genetics. 1987, New York: Columbia Univ. Press
Google Scholar
Watterson GA: On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975, 7: 256-276. 10.1016/0040-5809(75)90020-9.
Article
CAS
PubMed
Google Scholar
Librado P, Rozas J: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009, 25 (11): 1451-1452. 10.1093/bioinformatics/btp187.
Article
CAS
PubMed
Google Scholar
Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES: TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics. 2007, 23 (19): 2633-2645. 10.1093/bioinformatics/btm308.
Article
CAS
PubMed
Google Scholar
Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Copper R, Kwiatkowski D, Ward R, Lander ES: Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002, 419: 832-837. 10.1038/nature01140.
Article
CAS
PubMed
Google Scholar
Goldman N, Yang Z: A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution. 1994, 11: 725-736.
CAS
PubMed
Google Scholar
Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 2006, 4: 259-263. 10.1016/S1672-0229(07)60007-2.
Article
CAS
PubMed
Google Scholar
Crawford DL, Segal JA, Barnett JL: Evolutionary analysis of TATA-less proximal promoter function. Mol Biol Evol. 1999, 16 (2): 194-207.
Article
CAS
PubMed
Google Scholar
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M: An SNP caused loss of seed shattering during rice domestication. Science. 2006, 312: 1392-1395. 10.1126/science.1126410.
Article
CAS
PubMed
Google Scholar
Kariali E, Kuanar SR, Mohapatra PK: Individual tiller dynamics of two wild Oryza species in contrasting habitats. Plant Production Science. 2008, 11 (3): 355-360. 10.1626/pps.11.355.
Article
Google Scholar
Sasakawa H, Yamamoto Y: Comparison of the uptake of nitrate and ammonium by rice seedlings. Plant Physiology. 1978, 62 (4): 665-669. 10.1104/pp.62.4.665.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoshida S: Fundamentals of rice crop science. 1981, Philippines: The International Rice Research Institute
Google Scholar
Keith B, Dong XN, Ausubel FM, Fink GR: Differential induction of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase genes in Arabidopsis thaliana by wounding and pathogenic attack. Proc Nati Acad Sci USA. 1991, 88 (19): 8821-8825. 10.1073/pnas.88.19.8821.
Article
CAS
Google Scholar
Guo Y, Halfter U, Ishitani M, Zhu JK: Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance. The Plant Cell. 2001, 13: 1383-1400. 10.2307/3871302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vailleau F, Daniel X, Tronchet M, Montillet JL, Triantaphylides C, Roby D: A R2R3-MYB gene, AtMYB30, acts as a positive regulator of the hypersensitive cell death program in plant in response to pathogen attack. Proc Nati Acad Sci USA. 2002, 99 (15): 10179-10184. 10.1073/pnas.152047199.
Article
CAS
Google Scholar
Nagaoka S, Takano T: Salt tolerance-related protein STO binds to a Myb transcription factor homologue and confers salt tolerance in Arabidopsis. Journal of Experimental Botany. 2003, 54 (391): 2231-2237. 10.1093/jxb/erg241.
Article
CAS
PubMed
Google Scholar
Dunwell JM, Purvis A, Khuri S: Cupins: the most functionally diverse protein superfamily?. Phytochemistry. 2004, 65: 7-17. 10.1016/j.phytochem.2003.08.016.
Article
CAS
PubMed
Google Scholar
Gong ZZ, Dong CH, Lee H, Zhu JH, Xiong LM, Gong DM, Stevenson B, Zhu JK: A dead box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. The Plant Cell. 2005, 17: 256-267. 10.1105/tpc.104.027557.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gonzalez D, Bowen AJ, Carroll TS, Conlan RS: The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Molecular and Cellular Biology. 2007, 27 (15): 5306-5315. 10.1128/MCB.01912-06.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu B, Chen ZY, Song XW, Liu CY, Cui X, Zhao XF, Fang J, Xu WY, Zhang HY, Wang XJ, Chu CC, Deng XW, Xue YB, Cao XF: Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. The Plant Cell. 2007, 19 (9): 2705-2718. 10.1105/tpc.107.052209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma K, Xiao JH, Li XH, Zhang QF, Lian XM: Sequence and expression analysis of the C3HC4-type Ring finger gene family in rice. Gene. 2009, 444: 33-45. 10.1016/j.gene.2009.05.018.
Article
CAS
PubMed
Google Scholar
Lin ZW, Griffith ME, Li XR, Zhu ZF, Tan LB, Fu YC, Zhang WX, Wang XK, Xie DX, Sun CQ: Origin of seed shattering in rice (Oryza sativa L.). Planta. 2007, 226: 11-20. 10.1007/s00425-006-0460-4.
Article
CAS
PubMed
Google Scholar
Yamanaka S, Nakamura I, Watanabe KN, Sato YI: Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet. 2004, 108: 1200-1204. 10.1007/s00122-003-1564-x.
Article
CAS
PubMed
Google Scholar
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