These authors contributed equally to this work.
Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China
Article first published online: 29 OCT 2012
© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust
Volume 197, Issue 1, pages 290–299, January 2013
How to Cite
Sun, J., Qian, Q., Ma, D.-R., Xu, Z.-J., Liu, D., Du, H.-B. and Chen, W.-F. (2013), Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytologist, 197: 290–299. doi: 10.1111/nph.12012
- Issue published online: 26 NOV 2012
- Article first published online: 29 OCT 2012
- Manuscript Accepted: 20 SEP 2012
- Manuscript Received: 16 APR 2012
- National Natural Science Foundation of China (NSFC. Grant Number: 31271687
- China Agriculture Research System. Grant Number: CARS-01-13
- Open Subject of State Key Laboratory of Rice Biology. Grant Number: 090404
- Natural Science Foundation of Liaoning, China. Grant Number: 20102192
- 2001. Genetic diversity and population dynamics of weedy rice in Camargue area [France]. Genetics Selection Evolution 33: 425–440. , , .
- 2000. DNASTAR's Lasergene sequence analysis software. Methods in Molecular Biology 132: 71–91. .
- 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics 3: e163. , , , , , , , , , et al.
- 2006. Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in north-eastern China revealed by simple sequence repeat (SSR) markers. Annals of Botany 98: 1241–1252. , , , , , , .
- 2003. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Molecular Biology and Evolution 20: 67–75. , , , , , .
- 1872. Jiangbei Diary (in Chinese). .
- 1975. Weeds and domesticates: evolution in the man-made habitat. Economic Botany 29: 99–108. , .
- 2007. Weedy rices: origin, biology, ecology and control. Rome, Italy: FAO. , , .
- 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics 112: 1164–1171. , , , , , , , .
- 1999. Mechanical and chemical control of red rice (Oryza sativa L. var. sylvatica) in rice (Oryza sativa L.) pre-planting. Crop Protection 18: 251. , , , .
- 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631–1638. , , , , .
- 2002. Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Science 50: 333–339. , , .
- 2009. A strategy to provide long-term control of weedy rice while mitigating herbicide resistance transgene flow, and its potential use for other crops with related weeds. Pest Management Science 65: 723–731. , .
- 2010. Genetic perspectives on crop domestication. Trends in Plant Science 15: 529–537. , .
- 2010. Seeing red: the origin of grain pigmentation in US weedy rice. Molecular Ecology 19: 3380–3393. , , , , , .
- 2009. Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa). New Phytologist 184: 842–850. , , .
- 1992. Crops and man. Crop Science Society of America. Madison, WI, USA: American Society of Agronomy. .
- 1998. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Molecular Biology and Evolution 15: 978–987. , , .
- 1990. Varietal differences in longevity of tropical rough rice stored under ambient conditions. Seed Science and Technology 18: 361–369. , , .
- 2008. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars. Plant and Cell Physiology 49: 1283–1293. , , .
- 2006. An SNP caused loss of seed shattering during rice domestication. Science 312: 1392–1396. , , , , , , .
- 1967. Complementary genes Ph and Bh controlling ripening black coloration of rice hulls and their geographical distribution. Japanese Journal of Breeding 17: 13–19. , .
- 2003. Weed Management for Developing Countries (Addendum 1). Rome, Italy: FAO. .
- 2006. Rice domestication by reducing shattering. Science 311: 1936–1939. , , .
- 2011. Current situation and control strategy of weedy rice in China. China Plant Protection 31: 21–24 (in Chinese). , .
- 1921. The log of Zhuanghe County (in Chinese). , , .
- 2007. Origin of seed shattering in rice (Oryza sativa L.). Planta 226: 11–20. , , , , , , , , , .
- 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128. , .
- 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences, USA 103: 9578. , , , , .
- 2007. Origins and population genetics of weedy red rice in the USA. Molecular Ecology 16: 4523–4535. , .
- 2009. Efficient indica and japonica rice identification based on the InDel molecular method: its implication in rice breeding and evolutionary research. Progress in Natural Science 19: 1241–1252. , , .
- 2005. Gene flow from genetically modified rice and its environmental consequences. BioScience 55: 669–678. , .
- 1998. Six different plastid subtypes were found in O. sativa–O. rufipogon complex. Rice Genetics Newsletter 15: 80–81. , , , , , .
- 1972. Genetic distance between populations. American Naturalist 106: 283–292. .
- 1999. Red rice (Oryza sativa) biology. I. Characterization of red rice ecotypes. Weed Technology 13: 12–18. , , .
- 2009. The nature of selection during plant domestication. Nature 457: 843–848. , .
- 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology 10: 180. , , , , , .
- 2004. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology 135: 1198–1205. , , , , , , , , , et al.
- 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics 40: 1023–1028. , , , , , , .
- 1979. How to control the hard-to-kill weeds in rice. Weeds Today 10: 12–14. .
- 2010. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences, USA 107: 5792–5797. , , , , , , , , , et al.
- 2012. The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China. Theoretical and Applied Genetics 125: 1149–1157. , , , , , , , .
- 2007. Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics 3: e133. , , , , , , .
- 2006. Caught red-handed: Rc encodes a basic helix–loop–helix protein conditioning red pericarp in rice. Plant Cell 18: 283–294. , , , .
- 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596–1599. , , , .
- 2011. Utilization of weedy rice for development of japonica hybrid rice (Oryza sativa L.). Plant Science 180: 733–740. , , , , , .
- 2010. Molecular evolution of shattering loci in U.S. weedy rice. Molecular Ecology 19: 3271–3284. , , , , , .
- 2001. Is all red rice found in commercial rice really Oryza sativa? Weed Science 49: 468–476. , , , , , , .
- 2009. Breeding and pedigree of Chinese rice. Beijing, China: China Agriculture Press, 10: 312–314 (in Chinese). ,
- 2005. Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Research 12: 417–427. , , , .
- 2011. Rapid evolutionary divergence and ecotypic diversification of germination behavior in weedy rice populations. New Phytologist 191: 1119–1127. , , , , .
- 2009. Development of gene-tagged markers for quantitative trait loci underlying rice yield components. Euphytica 169: 215–226. , , , , , , , , , .
- 2005. Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochemical Genetics 43: 261–270. , , , , .
- 2008. Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell 20: 2946–2959. , , , , , , , , , .
- 2009. Selection on grain shattering genes and rates of rice domestication. New Phytologist 184: 708–720. , , , , , , .
- 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications 2: 467. , , , , , , , , , .
- 2010. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5: e10780. , , , , , , , , , .
- 2009. Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.). Journal of Genetics and Genomics 36: 435–442. , , , , .
- 2011. Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiology 155: 1301–1311. , , , , , , , , , et al.