TY - CHAP AU - Ziska, L. H. AU - Gealy, D. R. AU - Burgos, N. AU - Caicedo, A. L. AU - Gressel, J. AU - Lawton-Rauh, A. L. ED - Sparks, D. L. PY - 2015 DA - 2015// TI - Chapter three - weedy (red) rice: an emerging constraint to global rice production BT - Advances in Agronomy ID - Ziska2015 ER - TY - JOUR AU - Li, L. -. F. AU - Li, Y. -. L. AU - Jia, Y. AU - Caicedo, A. L. AU - Olsen, K. M. PY - 2017 DA - 2017// TI - Signatures of adaptation in the weedy rice genome JO - Nat Genet VL - 49 UR - https://doi.org/10.1038/ng.3825 DO - 10.1038/ng.3825 ID - Li2017 ER - TY - JOUR AU - Qiu, J. AU - Zhou, Y. AU - Mao, L. AU - Ye, C. AU - Wang, W. AU - Zhang, J. PY - 2017 DA - 2017// TI - Genomic variation associated with local adaptation of weedy rice during de-domestication JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/ncomms15323 DO - 10.1038/ncomms15323 ID - Qiu2017 ER - TY - JOUR AU - He, Q. AU - Kim, K. -. W. AU - Park, Y. -. J. PY - 2017 DA - 2017// TI - Population genomics identifies the origin and signatures of selection of Korean weedy rice JO - Plant Biotechnol J VL - 15 UR - https://doi.org/10.1111/pbi.12630 DO - 10.1111/pbi.12630 ID - He2017 ER - TY - JOUR AU - Sun, J. AU - Ma, D. AU - Tang, L. AU - Zhao, M. AU - Zhang, G. AU - Wang, W. PY - 2019 DA - 2019// TI - Population genomic analysis and de novo assembly reveal the origin of weedy rice as an evolutionary game JO - Mol Plant VL - 12 UR - https://doi.org/10.1016/j.molp.2019.01.019 DO - 10.1016/j.molp.2019.01.019 ID - Sun2019 ER - TY - JOUR AU - Wang, D. R. AU - Agosto-Pérez, F. J. AU - Chebotarov, D. AU - Shi, Y. AU - Marchini, J. AU - Fitzgerald, M. PY - 2018 DA - 2018// TI - An imputation platform to enhance integration of rice genetic resources JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-05538-1 DO - 10.1038/s41467-018-05538-1 ID - Wang2018 ER - TY - JOUR AU - Qi, X. AU - Liu, Y. AU - Vigueira, C. C. AU - Young, N. D. AU - Caicedo, A. L. AU - Jia, Y. PY - 2015 DA - 2015// TI - More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms JO - Mol Ecol VL - 24 UR - https://doi.org/10.1111/mec.13256 DO - 10.1111/mec.13256 ID - Qi2015 ER - TY - JOUR AU - Wedger, M. J. AU - Topp, C. N. AU - Olsen, K. M. PY - 2019 DA - 2019// TI - Convergent evolution of root system architecture in two independently evolved lineages of weedy rice JO - New Phytol VL - 223 UR - https://doi.org/10.1111/nph.15791 DO - 10.1111/nph.15791 ID - Wedger2019 ER - TY - JOUR AU - Huang, X. AU - Kurata, N. AU - Wei, X. AU - Wang, Z. -. X. AU - Wang, A. AU - Zhao, Q. PY - 2012 DA - 2012// TI - A map of rice genome variation reveals the origin of cultivated rice JO - Nature. VL - 490 UR - https://doi.org/10.1038/nature11532 DO - 10.1038/nature11532 ID - Huang2012 ER - TY - JOUR AU - Wang, W. AU - Mauleon, R. AU - Hu, Z. AU - Chebotarov, D. AU - Tai, S. AU - Wu, Z. PY - 2018 DA - 2018// TI - Genomic variation in 3,010 diverse accessions of Asian cultivated rice JO - Nature. VL - 557 UR - https://doi.org/10.1038/s41586-018-0063-9 DO - 10.1038/s41586-018-0063-9 ID - Wang2018 ER - TY - JOUR AU - Song, B. -. K. AU - Chuah, T. -. S. AU - Tam, S. M. AU - Olsen, K. M. PY - 2014 DA - 2014// TI - Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia JO - Mol Ecol VL - 23 UR - https://doi.org/10.1111/mec.12922 DO - 10.1111/mec.12922 ID - Song2014 ER - TY - JOUR AU - Vigueira, C. C. AU - Qi, X. AU - Song, B. -. K. AU - Li, L. -. F. AU - Caicedo, A. L. AU - Jia, Y. PY - 2019 DA - 2019// TI - Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia JO - Evol Appl VL - 12 UR - https://doi.org/10.1111/eva.12581 DO - 10.1111/eva.12581 ID - Vigueira2019 ER - TY - JOUR AU - Wedger, M. J. AU - Pusadee, T. AU - Wongtamee, A. AU - Olsen, K. M. PY - 2019 DA - 2019// TI - Discordant patterns of introgression suggest historical gene flow into Thai weedy rice from domesticated and wild relatives JO - J Hered VL - 110 UR - https://doi.org/10.1093/jhered/esz030 DO - 10.1093/jhered/esz030 ID - Wedger2019 ER - TY - JOUR AU - Chen, E. AU - Huang, X. AU - Tian, Z. AU - Wing, R. A. AU - Han, B. PY - 2019 DA - 2019// TI - The genomics of Oryza species provides insights into rice domestication and heterosis JO - Annu Rev Plant Biol VL - 70 UR - https://doi.org/10.1146/annurev-arplant-050718-100320 DO - 10.1146/annurev-arplant-050718-100320 ID - Chen2019 ER - TY - STD TI - Roso AC, Jr AM, Delatorre CA, Menezes VG. Regional scale distribution of imidazolinone herbicide-resistant alleles in red rice (Oryza sativa L.) determined through SNP markers. Field Crops Res. 2010;119:175–82. ID - ref15 ER - TY - JOUR AU - Scarabel, L. AU - Cenghialta, C. AU - Manuello, D. AU - Sattin, M. PY - 2012 DA - 2012// TI - Monitoring and management of imidazolinone-resistant red rice (Oryza sativa L., var. sylvatica) in Clearfield® Italian Paddy Rice JO - Agronomy VL - 2 UR - https://doi.org/10.3390/agronomy2040371 DO - 10.3390/agronomy2040371 ID - Scarabel2012 ER - TY - JOUR AU - Merotto, A. AU - Goulart, I. C. G. R. AU - Nunes, A. L. AU - Kalsing, A. AU - Markus, C. AU - Menezes, V. G. PY - 2016 DA - 2016// TI - Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil JO - Evol Appl VL - 9 UR - https://doi.org/10.1111/eva.12387 DO - 10.1111/eva.12387 ID - Merotto2016 ER - TY - JOUR AU - Goulart, I. AU - Borba, T. C. O. AU - Menezes, V. G. AU - Merotto, A. PY - 2014 DA - 2014// TI - Distribution of weedy red rice (Oryza sativa) resistant to imidazolinone herbicides and its relationship to rice cultivars and wild Oryza species JO - Weed Sci VL - 62 UR - https://doi.org/10.1614/WS-D-13-00126.1 DO - 10.1614/WS-D-13-00126.1 ID - Goulart2014 ER - TY - JOUR AU - Reagon, M. AU - Thurber, C. S. AU - Gross, B. L. AU - Olsen, K. M. AU - Jia, Y. AU - Caicedo, A. L. PY - 2010 DA - 2010// TI - Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice JO - BMC Evol Biol VL - 10 UR - https://doi.org/10.1186/1471-2148-10-180 DO - 10.1186/1471-2148-10-180 ID - Reagon2010 ER - TY - JOUR AU - Huang, Z. AU - Young, N. D. AU - Reagon, M. AU - Hyma, K. E. AU - Olsen, K. M. AU - Jia, Y. PY - 2017 DA - 2017// TI - All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza JO - Mol Ecol VL - 26 UR - https://doi.org/10.1111/mec.14120 DO - 10.1111/mec.14120 ID - Huang2017 ER - TY - JOUR AU - Gu, X. -. Y. AU - Foley, M. E. AU - Horvath, D. P. AU - Anderson, J. V. AU - Feng, J. AU - Zhang, L. PY - 2011 DA - 2011// TI - Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice JO - Genetics. VL - 189 UR - https://doi.org/10.1534/genetics.111.131169 DO - 10.1534/genetics.111.131169 ID - Gu2011 ER - TY - JOUR AU - Sweeney, M. T. AU - Thomson, M. J. AU - Pfeil, B. E. AU - McCouch, S. PY - 2006 DA - 2006// TI - Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.105.038430 DO - 10.1105/tpc.105.038430 ID - Sweeney2006 ER - TY - JOUR AU - Cui, Y. AU - Song, B. K. AU - Li, L. -. F. AU - Li, Y. -. L. AU - Huang, Z. AU - Caicedo, A. L. PY - 2016 DA - 2016// TI - Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice JO - G3 VL - 6 UR - https://doi.org/10.1534/g3.116.035881 DO - 10.1534/g3.116.035881 ID - Cui2016 ER - TY - JOUR AU - Kader, J. -. C. PY - 1996 DA - 1996// TI - Lipid-transfer proteins in plants JO - Annu Rev Plant Physiol Plant Mol Biol VL - 47 UR - https://doi.org/10.1146/annurev.arplant.47.1.627 DO - 10.1146/annurev.arplant.47.1.627 ID - Kader1996 ER - TY - JOUR AU - Guo, X. AU - Hou, X. AU - Fang, J. AU - Wei, P. AU - Xu, B. AU - Chen, M. PY - 2013 DA - 2013// TI - The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism JO - Plant J VL - 75 UR - https://doi.org/10.1111/tpj.12209 DO - 10.1111/tpj.12209 ID - Guo2013 ER - TY - JOUR AU - Peng, S. AU - Tang, Q. AU - Zou, Y. PY - 2009 DA - 2009// TI - Current status and challenges of rice production in China JO - Plant Prod Sci VL - 12 UR - https://doi.org/10.1626/pps.12.3 DO - 10.1626/pps.12.3 ID - Peng2009 ER - TY - JOUR AU - Morishima, H. AU - Sano, Y. AU - Oka, H. I. PY - 1984 DA - 1984// TI - Differentiation of perennial and annual types due to habitat conditions in the wild rice Oryza perennis JO - Plant Syst Evol VL - 144 UR - https://doi.org/10.1007/BF00986670 DO - 10.1007/BF00986670 ID - Morishima1984 ER - TY - JOUR AU - Neik, T. X. AU - Chai, J. -. Y. AU - Tan, S. -. Y. AU - Sudo, M. P. S. AU - Cui, Y. AU - Jayaraj, J. PY - 2019 DA - 2019// TI - When west meets east: the origins and spread of weedy rice between continental and island Southeast Asia JO - G3 VL - 9 UR - https://doi.org/10.1534/g3.119.400021 DO - 10.1534/g3.119.400021 ID - Neik2019 ER - TY - JOUR AU - Patel, R. K. AU - Jain, M. PY - 2012 DA - 2012// TI - NGS QC toolkit: a toolkit for quality control of next generation sequencing data JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0030619 DO - 10.1371/journal.pone.0030619 ID - Patel2012 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - McKenna, A. AU - Hanna, M. AU - Banks, E. AU - Sivachenko, A. AU - Cibulskis, K. AU - Kernytsky, A. PY - 2010 DA - 2010// TI - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - JOUR AU - Cingolani, P. AU - Platts, A. AU - Wang, L. L. AU - Coon, M. AU - Nguyen, T. AU - Wang, L. PY - 2012 DA - 2012// TI - A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 JO - Fly. VL - 6 UR - https://doi.org/10.4161/fly.19695 DO - 10.4161/fly.19695 ID - Cingolani2012 ER - TY - JOUR AU - Browning, S. R. AU - Browning, B. L. PY - 2007 DA - 2007// TI - Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering JO - Am J Hum Genet VL - 81 UR - https://doi.org/10.1086/521987 DO - 10.1086/521987 ID - Browning2007 ER - TY - JOUR AU - Zheng, X. AU - Levine, D. AU - Shen, J. AU - Gogarten, S. M. AU - Laurie, C. AU - Weir, B. S. PY - 2012 DA - 2012// TI - A high-performance computing toolset for relatedness and principal component analysis of SNP data JO - Bioinformatics. VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts606 DO - 10.1093/bioinformatics/bts606 ID - Zheng2012 ER - TY - JOUR AU - Raj, A. AU - Stephens, M. AU - Pritchard, J. K. PY - 2014 DA - 2014// TI - fastSTRUCTURE: variational inference of population structure in large SNP data sets JO - Genetics. VL - 197 UR - https://doi.org/10.1534/genetics.114.164350 DO - 10.1534/genetics.114.164350 ID - Raj2014 ER - TY - JOUR AU - Price, M. N. AU - Dehal, P. S. AU - Arkin, A. P. PY - 2009 DA - 2009// TI - FastTree: computing large minimum evolution trees with profiles instead of a distance matrix JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp077 DO - 10.1093/molbev/msp077 ID - Price2009 ER - TY - JOUR AU - Wang, M. AU - Yu, Y. AU - Haberer, G. AU - Marri, P. R. AU - Fan, C. AU - Goicoechea, J. L. PY - 2014 DA - 2014// TI - The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.3044 DO - 10.1038/ng.3044 ID - Wang2014 ER - TY - JOUR AU - Bradbury, P. J. AU - Zhang, Z. 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 - Danecek, P. AU - Auton, A. AU - Abecasis, G. AU - Albers, C. A. AU - Banks, E. AU - DePristo, M. A. PY - 2011 DA - 2011// TI - The variant call format and VCFtools JO - Bioinformatics. VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr330 DO - 10.1093/bioinformatics/btr330 ID - Danecek2011 ER - TY - JOUR AU - Terhorst, J. AU - Kamm, J. A. AU - Song, Y. S. PY - 2017 DA - 2017// TI - Robust and scalable inference of population history from hundreds of unphased whole genomes JO - Nat Genet VL - 49 UR - https://doi.org/10.1038/ng.3748 DO - 10.1038/ng.3748 ID - Terhorst2017 ER - TY - JOUR AU - Molina, J. AU - Sikora, M. AU - Garud, N. AU - Flowers, J. M. AU - Rubinstein, S. AU - Reynolds, A. PY - 2011 DA - 2011// TI - Molecular evidence for a single evolutionary origin of domesticated rice JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1104686108 DO - 10.1073/pnas.1104686108 ID - Molina2011 ER - TY - JOUR AU - Green, R. E. AU - Krause, J. AU - Briggs, A. W. AU - Maricic, T. AU - Stenzel, U. AU - Kircher, M. PY - 2010 DA - 2010// TI - A draft sequence of the Neandertal genome JO - Science. VL - 328 UR - https://doi.org/10.1126/science.1188021 DO - 10.1126/science.1188021 ID - Green2010 ER - TY - JOUR AU - Pickrell, J. K. AU - Pritchard, J. K. PY - 2012 DA - 2012// TI - Inference of population splits and mixtures from genome-wide allele frequency data JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002967 DO - 10.1371/journal.pgen.1002967 ID - Pickrell2012 ER - TY - JOUR AU - Tian, T. AU - Liu, Y. AU - Yan, H. AU - You, Q. AU - Yi, X. AU - Du, Z. PY - 2017 DA - 2017// TI - agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkx382 DO - 10.1093/nar/gkx382 ID - Tian2017 ER - TY - BOOK AU - Qiu, J. AU - Jia, L. AU - Wu, D. Y. AU - Weng, X. F. AU - Chen, L. J. AU - Sun, J. PY - 2020 DA - 2020// TI - Global weedy rice research project. Sequence Read Archive ID - Qiu2020 ER - TY - BOOK AU - Qiu, J. AU - Jia, L. AU - Wu, D. Y. AU - Weng, X. F. AU - Chen, L. J. AU - Sun, J. PY - 2020 DA - 2020// TI - Origin of weedy rice in Japan. Sequence Read Archive ID - Qiu2020 ER -