TY - JOUR AU - Ma, J. AU - Bennetzen, J. L. PY - 2004 DA - 2004// TI - Rapid recent growth and divergence of rice nuclear genomes JO - Proc Nati Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0403715101 DO - 10.1073/pnas.0403715101 ID - Ma2004 ER - TY - JOUR AU - Panaud, C. R. PY - 2009 DA - 2009// TI - The molecular bases of cereal domestication and the history of rice JO - Biologies VL - 332 UR - https://doi.org/10.1016/j.crvi.2008.09.003 DO - 10.1016/j.crvi.2008.09.003 ID - Panaud2009 ER - TY - JOUR AU - Garris, A. J. AU - Tai, T. H. AU - Coburn, J. AU - Kresovich, S. AU - McCouch, S. R. PY - 2005 DA - 2005// TI - Genetic structure and diversity in Oryza sativa L JO - Genetics VL - 169 UR - https://doi.org/10.1534/genetics.104.035642 DO - 10.1534/genetics.104.035642 ID - Garris2005 ER - TY - JOUR AU - McCouch, S. R. AU - Sweeney, M. AU - Li, J. M. AU - Jiang, H. AU - Thomson, M. AU - Septiningsih, E. AU - Edwards, J. AU - Moncada, P. AU - Xiao, J. H. AU - Garris, A. AU - Tai, T. AU - Martinez, C. AU - Tohme, J. AU - Sugiono, M. AU - McClung, A. AU - Yuan, L. P. AU - Ahn, S. PY - 2006 DA - 2006// TI - Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa JO - Euphytica VL - 154 UR - https://doi.org/10.1007/s10681-006-9210-8 DO - 10.1007/s10681-006-9210-8 ID - McCouch2006 ER - TY - JOUR AU - Tanksley, S. D. AU - McCouch, S. R. PY - 1997 DA - 1997// TI - Seed banks and molecular maps: unlocking genetic potential from the wild JO - Science VL - 277 UR - https://doi.org/10.1126/science.277.5329.1063 DO - 10.1126/science.277.5329.1063 ID - Tanksley1997 ER - TY - JOUR AU - Caicedo, A. L. AU - Williamson, S. H. AU - Hernandez, R. D. AU - Boyko, A. AU - Fledel-Alon, A. AU - York, T. L. AU - Polato, N. R. AU - Olsen, K. M. AU - Nielsen, R. AU - McCouch, S. R. AU - Bustamante, C. D. AU - Purugganan, M. D. PY - 2007 DA - 2007// TI - Genome-wide patterns of nucleotide polymorphism in domesticated rice JO - PLOS Genetics VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030163 DO - 10.1371/journal.pgen.0030163 ID - Caicedo2007 ER - TY - JOUR AU - Zhu, Q. H. AU - Zheng, X. M. AU - Luo, J. C. AU - Gaut, B. S. AU - Ge, S. PY - 2007 DA - 2007// TI - Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm005 DO - 10.1093/molbev/msm005 ID - Zhu2007 ER - TY - JOUR AU - Li, C. AU - Zhou, A. AU - Sang, T. PY - 2006 DA - 2006// TI - Rice domestication by reducing shattering JO - Science VL - 311 UR - https://doi.org/10.1126/science.1123604 DO - 10.1126/science.1123604 ID - Li2006 ER - TY - JOUR AU - Sang, T. AU - Ge, S. PY - 2007 DA - 2007// TI - Genetics and phylogenetics of rice domestication JO - Current Opinion in Genetics and Development VL - 17 UR - https://doi.org/10.1016/j.gde.2007.09.005 DO - 10.1016/j.gde.2007.09.005 ID - Sang2007 ER - TY - JOUR AU - Zhang, L. B. AU - Zhu, Q. H. AU - Wu, Z. Q. AU - Ibarra, J. R. AU - Gaut, B. S. AU - Ge, S. AU - Sang, T. PY - 2009 DA - 2009// TI - Selection on grain shattering genes and rates of rice domestication JO - New Phytologist VL - 184 UR - https://doi.org/10.1111/j.1469-8137.2009.02984.x DO - 10.1111/j.1469-8137.2009.02984.x ID - Zhang2009 ER - TY - JOUR AU - Olsen, K. M. AU - Caicedo, A. L. AU - Polato, N. AU - McClung, A. AU - McCouch, S. AU - Purugganan, M. D. PY - 2006 DA - 2006// TI - Selection under domestication: evidence for a sweep in the rice waxy genomic region JO - Genetics VL - 173 UR - https://doi.org/10.1534/genetics.106.056473 DO - 10.1534/genetics.106.056473 ID - Olsen2006 ER - TY - JOUR AU - Sweeney, M. T. AU - Thomson, M. J. AU - Cho, Y. G. AU - Park, Y. J. AU - Williamson, S. H. AU - Bustamante, C. D. AU - McCouch, S. R. PY - 2007 DA - 2007// TI - Global dissemination of a single mutation conferring white pericarp in rice JO - PLOS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030133 DO - 10.1371/journal.pgen.0030133 ID - Sweeney2007 ER - TY - JOUR AU - Wang, R. L. AU - Stec, A. AU - Hey, J. AU - Lukens, L. AU - Doebley, J. PY - 1999 DA - 1999// TI - The limits of selection during maize domestication JO - Nature VL - 398 UR - https://doi.org/10.1038/18435 DO - 10.1038/18435 ID - Wang1999 ER - TY - JOUR AU - Doebley, J. AU - Stec, A. AU - Hubbard, L. PY - 1997 DA - 1997// TI - The evolution of apical dominance in maize JO - Natrue VL - 386 UR - https://doi.org/10.1038/386485a0 DO - 10.1038/386485a0 ID - Doebley1997 ER - TY - JOUR AU - Clark, R. M. AU - Linton, E. AU - Messing, J. AU - Doebley, J. F. PY - 2002 DA - 2002// TI - Pattern of diversity in the genomic region near the maize domestication gene tb1 JO - Proc Nati Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.2237049100 DO - 10.1073/pnas.2237049100 ID - Clark2002 ER - TY - JOUR AU - Palaisa, K. A. AU - Morgante, M. AU - Williams, M. AU - Rafalski, A. PY - 2003 DA - 2003// TI - Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci JO - The Plant Cell VL - 15 UR - https://doi.org/10.1105/tpc.012526 DO - 10.1105/tpc.012526 ID - Palaisa2003 ER - TY - JOUR AU - Palaisa, K. AU - Morgante, M. AU - Tingey, S. AU - Rafalski, A. PY - 2004 DA - 2004// TI - Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep JO - Proc Nati Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0307839101 DO - 10.1073/pnas.0307839101 ID - Palaisa2004 ER - TY - JOUR AU - Wang, M. Y. AU - Siddiqi, M. Y. AU - Ruth, T. J. AU - Glass, A. D. M. PY - 1993 DA - 1993// TI - Ammonium uptake by rice roots (II. Kinetics of 13NH4+ influx across the plasmalemma) JO - Plant Physiology VL - 103 UR - https://doi.org/10.1104/pp.103.4.1463 DO - 10.1104/pp.103.4.1463 ID - Wang1993 ER - TY - JOUR AU - Kronzucker, H. J. AU - Glass, A. D. M. AU - Siddiqi, M. Y. PY - 1996 DA - 1996// TI - Kinetics of NH4+ influx in spruce JO - Plant Physiology VL - 110 ID - Kronzucker1996 ER - TY - JOUR AU - Loque, D. AU - von Wiren, N. PY - 2004 DA - 2004// TI - Regulatory levels for the transport of ammonium in plant roots JO - Journal of Experimental Botany VL - 55 UR - https://doi.org/10.1093/jxb/erh147 DO - 10.1093/jxb/erh147 ID - Loque2004 ER - TY - JOUR AU - Li, B. Z. AU - Mike, M. AU - Li, S. M. AU - Li, H. Y. AU - Zhu, S. W. AU - Shi, W. M. AU - Su, Y. H. PY - 2009 DA - 2009// TI - Molecular basis and regulation of ammonium transporter in rice JO - Rice Science VL - 16 UR - https://doi.org/10.1016/S1672-6308(08)60096-7 DO - 10.1016/S1672-6308(08)60096-7 ID - Li2009 ER - TY - JOUR AU - Kaiser, B. N. AU - Rawat, S. R. AU - Siddiqi, M. Y. AU - Masle, J. AU - Glass, A. D. PY - 2002 DA - 2002// TI - Functional analysis of an Arabidopsis T-DNA 'Knockout' of the high-affinity NH4+ transporter AtAMT1;1 JO - Plant Physiology VL - 130 UR - https://doi.org/10.1104/pp.102.010843 DO - 10.1104/pp.102.010843 ID - Kaiser2002 ER - TY - JOUR AU - Salvemini, F. AU - Marini, A. M. AU - Riccio, A. AU - Patriarca, E. J. AU - Chiurazzi, M. PY - 2001 DA - 2001// TI - Functional characterization of an ammonium transporter gene from Lotus japonicus JO - Gene VL - 270 UR - https://doi.org/10.1016/S0378-1119(01)00470-X DO - 10.1016/S0378-1119(01)00470-X ID - Salvemini2001 ER - TY - JOUR AU - Ludewig, U. AU - Wilken, S. AU - Wu, B. AU - Jost, W. AU - Obrdlik, P. AU - Ei Bakkoury, M. AU - Marini, A. M. AU - Andre, B. AU - Hamacher, T. AU - Boles, E. AU - von Wiren, N. AU - Frommer, W. B. PY - 2003 DA - 2003// TI - Homo- and hetero-oligomerization of ammonium transporter-1 NH4+ uniporters JO - The Journal of Biological Chemistry VL - 278 UR - https://doi.org/10.1074/jbc.M307424200 DO - 10.1074/jbc.M307424200 ID - Ludewig2003 ER - TY - JOUR AU - Loque, D. AU - Yuan, L. X. AU - Kojima, S. AU - Gojon, A. AU - Wirth, J. AU - Gazzarrini, S. AU - Ishiyama, K. AU - Takahashi, H. AU - von Wiren, N. PY - 2006 DA - 2006// TI - Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis root JO - The Plant Journal VL - 48 UR - https://doi.org/10.1111/j.1365-313X.2006.02887.x DO - 10.1111/j.1365-313X.2006.02887.x ID - Loque2006 ER - TY - JOUR AU - Yuan, L. X. AU - Loque, D. AU - Kojima, S. AU - Rauch, S. AU - Ishiyama, K. AU - Inoue, E. AU - Takahashi, H. AU - von Wiren, N. PY - 2007 DA - 2007// TI - The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial arrangement and biochemical properties of AMT1-type transporters JO - The Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.052134 DO - 10.1105/tpc.107.052134 ID - Yuan2007 ER - TY - JOUR AU - Kumar, A. AU - Silim, S. N. AU - Okamoto, M. AU - Siddiqi, M. Y. AU - Glass, A. D. M. PY - 2003 DA - 2003// TI - Differential expression of three members of the AMT1 gene family encoding putative high-affinity NH4+ transporters in roots of Oryza sativa subspecies indica JO - Plant, Cell and Environment VL - 26 UR - https://doi.org/10.1046/j.1365-3040.2003.01023.x DO - 10.1046/j.1365-3040.2003.01023.x ID - Kumar2003 ER - TY - JOUR AU - Sonoda, Y. AU - Ikeda, A. AU - Saiki, S. AU - von Wiren, N. AU - Yamaya, T. AU - Yamaguchi, J. PY - 2003 DA - 2003// TI - Distinct expression and function of three ammonium transporter genes (OsAMT1;1-1;3) in rice JO - Plant Cell Physiology VL - 44 UR - https://doi.org/10.1093/pcp/pcg083 DO - 10.1093/pcp/pcg083 ID - Sonoda2003 ER - TY - JOUR AU - Sonoda, Y. AU - Ikeda, A. AU - Saiki, S. AU - Yamaya, T. AU - Yamaguchi, J. PY - 2003 DA - 2003// TI - Feedback regulation of the ammonium transporter gene family AMT1 by glutamine in rice JO - Plant Cell Physiology VL - 44 UR - https://doi.org/10.1093/pcp/pcg169 DO - 10.1093/pcp/pcg169 ID - Sonoda2003 ER - TY - JOUR AU - Wen, W. W. AU - Mei, H. W. AU - Feng, F. J. AU - Yu, S. B. AU - Huang, Z. C. AU - Wu, J. H. AU - Chen, L. AU - Xu, X. Y. AU - Luo, L. J. PY - 2009 DA - 2009// TI - Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.) JO - Theor Appl Genet VL - 119 UR - https://doi.org/10.1007/s00122-009-1052-z DO - 10.1007/s00122-009-1052-z ID - Wen2009 ER - TY - JOUR AU - Rogers, S. O. AU - Bendich, A. J. PY - 1988 DA - 1988// TI - Extraction of DNA from plant tissue JO - Plant Mol Biol Manual VL - A6 ID - Rogers1988 ER - TY - CHAP AU - Nei, M. PY - 1987 DA - 1987// BT - Molecular Evolutionary Genetics PB - Columbia Univ. Press CY - New York ID - Nei1987 ER - TY - JOUR AU - Watterson, G. A. PY - 1975 DA - 1975// TI - On the number of segregating sites in genetical models without recombination JO - Theor Popul Biol VL - 7 UR - https://doi.org/10.1016/0040-5809(75)90020-9 DO - 10.1016/0040-5809(75)90020-9 ID - Watterson1975 ER - TY - JOUR AU - Librado, P. AU - Rozas, J. PY - 2009 DA - 2009// TI - DnaSP v5: A software for comprehensive analysis of DNA polymorphism data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp187 DO - 10.1093/bioinformatics/btp187 ID - Librado2009 ER - TY - JOUR AU - Bradbury, P. J. AU - Zhang, Z. W. AU - Kroon, D. E. AU - Casstevens, T. M. AU - Ramdoss, Y. AU - Buckler, E. S. PY - 2007 DA - 2007// TI - TASSEL: Software for association mapping of complex traits in diverse samples JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm308 DO - 10.1093/bioinformatics/btm308 ID - Bradbury2007 ER - TY - JOUR AU - Sabeti, P. C. AU - Reich, D. E. AU - Higgins, J. M. AU - Levine, H. Z. AU - Richter, D. J. AU - Schaffner, S. F. AU - Gabriel, S. B. AU - Platko, J. V. AU - Patterson, N. J. AU - McDonald, G. J. AU - Ackerman, H. C. AU - Campbell, S. J. AU - Altshuler, D. AU - Copper, R. AU - Kwiatkowski, D. AU - Ward, R. AU - Lander, E. S. PY - 2002 DA - 2002// TI - Detecting recent positive selection in the human genome from haplotype structure JO - Nature VL - 419 UR - https://doi.org/10.1038/nature01140 DO - 10.1038/nature01140 ID - Sabeti2002 ER - TY - JOUR AU - Goldman, N. AU - Yang, Z. PY - 1994 DA - 1994// TI - A codon-based model of nucleotide substitution for protein-coding DNA sequences JO - Molecular Biology and Evolution VL - 11 ID - Goldman1994 ER - TY - JOUR AU - Zhang, Z. AU - Li, J. AU - Zhao, X. Q. AU - Wang, J. AU - Wong, G. K. AU - Yu, J. PY - 2006 DA - 2006// TI - KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging JO - Genomics Proteomics Bioinformatics VL - 4 UR - https://doi.org/10.1016/S1672-0229(07)60007-2 DO - 10.1016/S1672-0229(07)60007-2 ID - Zhang2006 ER - TY - JOUR AU - Crawford, D. L. AU - Segal, J. A. AU - Barnett, J. L. PY - 1999 DA - 1999// TI - Evolutionary analysis of TATA-less proximal promoter function JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026102 DO - 10.1093/oxfordjournals.molbev.a026102 ID - Crawford1999 ER - TY - JOUR AU - Konishi, S. AU - Izawa, T. AU - Lin, S. Y. AU - Ebana, K. AU - Fukuta, Y. AU - Sasaki, T. AU - Yano, M. PY - 2006 DA - 2006// TI - An SNP caused loss of seed shattering during rice domestication JO - Science VL - 312 UR - https://doi.org/10.1126/science.1126410 DO - 10.1126/science.1126410 ID - Konishi2006 ER - TY - JOUR AU - Kariali, E. AU - Kuanar, S. R. AU - Mohapatra, P. K. PY - 2008 DA - 2008// TI - Individual tiller dynamics of two wild Oryza species in contrasting habitats JO - Plant Production Science VL - 11 UR - https://doi.org/10.1626/pps.11.355 DO - 10.1626/pps.11.355 ID - Kariali2008 ER - TY - JOUR AU - Sasakawa, H. AU - Yamamoto, Y. PY - 1978 DA - 1978// TI - Comparison of the uptake of nitrate and ammonium by rice seedlings JO - Plant Physiology VL - 62 UR - https://doi.org/10.1104/pp.62.4.665 DO - 10.1104/pp.62.4.665 ID - Sasakawa1978 ER - TY - CHAP AU - Yoshida, S. PY - 1981 DA - 1981// BT - Fundamentals of rice crop science PB - The International Rice Research Institute CY - Philippines ID - Yoshida1981 ER - TY - JOUR AU - Keith, B. AU - Dong, X. N. AU - Ausubel, F. M. AU - Fink, G. R. PY - 1991 DA - 1991// TI - Differential induction of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase genes in Arabidopsis thaliana by wounding and pathogenic attack JO - Proc Nati Acad Sci USA VL - 88 UR - https://doi.org/10.1073/pnas.88.19.8821 DO - 10.1073/pnas.88.19.8821 ID - Keith1991 ER - TY - JOUR AU - Guo, Y. AU - Halfter, U. AU - Ishitani, M. AU - Zhu, J. K. PY - 2001 DA - 2001// TI - Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance JO - The Plant Cell VL - 13 UR - https://doi.org/10.1105/tpc.13.6.1383 DO - 10.1105/tpc.13.6.1383 ID - Guo2001 ER - TY - JOUR AU - Vailleau, F. AU - Daniel, X. AU - Tronchet, M. AU - Montillet, J. L. AU - Triantaphylides, C. AU - Roby, D. PY - 2002 DA - 2002// TI - A R2R3-MYB gene, AtMYB30, acts as a positive regulator of the hypersensitive cell death program in plant in response to pathogen attack JO - Proc Nati Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.152047199 DO - 10.1073/pnas.152047199 ID - Vailleau2002 ER - TY - JOUR AU - Nagaoka, S. AU - Takano, T. PY - 2003 DA - 2003// TI - Salt tolerance-related protein STO binds to a Myb transcription factor homologue and confers salt tolerance in Arabidopsis JO - Journal of Experimental Botany VL - 54 UR - https://doi.org/10.1093/jxb/erg241 DO - 10.1093/jxb/erg241 ID - Nagaoka2003 ER - TY - JOUR AU - Dunwell, J. M. AU - Purvis, A. AU - Khuri, S. PY - 2004 DA - 2004// TI - Cupins: the most functionally diverse protein superfamily? JO - Phytochemistry VL - 65 UR - https://doi.org/10.1016/j.phytochem.2003.08.016 DO - 10.1016/j.phytochem.2003.08.016 ID - Dunwell2004 ER - TY - JOUR AU - Gong, Z. Z. AU - Dong, C. H. AU - Lee, H. AU - Zhu, J. H. AU - Xiong, L. M. AU - Gong, D. M. AU - Stevenson, B. AU - Zhu, J. K. PY - 2005 DA - 2005// TI - A dead box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis JO - The Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.104.027557 DO - 10.1105/tpc.104.027557 ID - Gong2005 ER - TY - JOUR AU - Gonzalez, D. AU - Bowen, A. J. AU - Carroll, T. S. AU - Conlan, R. S. PY - 2007 DA - 2007// TI - The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription JO - Molecular and Cellular Biology VL - 27 UR - https://doi.org/10.1128/MCB.01912-06 DO - 10.1128/MCB.01912-06 ID - Gonzalez2007 ER - TY - JOUR AU - Liu, B. AU - Chen, Z. Y. AU - Song, X. W. AU - Liu, C. Y. AU - Cui, X. AU - Zhao, X. F. AU - Fang, J. AU - Xu, W. Y. AU - Zhang, H. Y. AU - Wang, X. J. AU - Chu, C. C. AU - Deng, X. W. AU - Xue, Y. B. AU - Cao, X. F. PY - 2007 DA - 2007// TI - Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development JO - The Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.052209 DO - 10.1105/tpc.107.052209 ID - Liu2007 ER - TY - JOUR AU - Ma, K. AU - Xiao, J. H. AU - Li, X. H. AU - Zhang, Q. F. AU - Lian, X. M. PY - 2009 DA - 2009// TI - Sequence and expression analysis of the C3HC4-type Ring finger gene family in rice JO - Gene VL - 444 UR - https://doi.org/10.1016/j.gene.2009.05.018 DO - 10.1016/j.gene.2009.05.018 ID - Ma2009 ER - TY - JOUR AU - Lin, Z. W. AU - Griffith, M. E. AU - Li, X. R. AU - Zhu, Z. F. AU - Tan, L. B. AU - Fu, Y. C. AU - Zhang, W. X. AU - Wang, X. K. AU - Xie, D. X. AU - Sun, C. Q. PY - 2007 DA - 2007// TI - Origin of seed shattering in rice (Oryza sativa L.) JO - Planta VL - 226 UR - https://doi.org/10.1007/s00425-006-0460-4 DO - 10.1007/s00425-006-0460-4 ID - Lin2007 ER - TY - JOUR AU - Yamanaka, S. AU - Nakamura, I. AU - Watanabe, K. N. AU - Sato, Y. I. PY - 2004 DA - 2004// TI - Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice JO - Theor Appl Genet VL - 108 UR - https://doi.org/10.1007/s00122-003-1564-x DO - 10.1007/s00122-003-1564-x ID - Yamanaka2004 ER -