Abstract
The domestication of crops involves a complex process of selection in plant evolution and is associated with changes in the DNA regulating agronomically important traits. Here we report the cloning of a newly identified QTL, qSW5 (QTL for seed width on chromosome 5), involved in the determination of grain width in rice. Through fine mapping, complementation testing and association analysis, we found that a deletion in qSW5 resulted in a significant increase in sink size owing to an increase in cell number in the outer glume of the rice flower; this trait might have been selected by ancient humans to increase yield of rice grains. In addition, we mapped two other defective functional nucleotide polymorphisms of rice domestication-related genes with genome-wide RFLP polymorphisms of various rice landraces. These analyses show that the qSW5 deletion had an important historical role in artificial selection, propagation of cultivation and natural crossings in rice domestication, and shed light on how the rice genome was domesticated.
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References
Darwin, C. The Variations of Animals and Plants under Domestication (D. Appleton, New York, 1857).
Wright, S.I. et al. The effects of artificial selection on the maize genome. Science 308, 1310–1314 (2005).
Doebley, J.F., Gaut, B.S. & Smith, B.D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).
Roos-Ibarra, J., Morell, P.L. & Gaut, B.S. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc. Natl. Acad. Sci. USA 104, 8641–8648 (2007).
Dubcovsky, J. & Dvorak, J. Genome plasticity: a key factor in the success of polyploidy wheat under domestication. Science 316, 1862–1866 (2007).
Sang, T. & Ge, S. The puzzle of rice domestication. J. Integr. Plant Biol. 49, 760–768 (2007).
Sweeney, M. & McCouch, S. The complex history of the domestication of rice. Ann. Bot. (Lond.) 100, 951–957 (2007).
Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).
Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).
Simons, K.J. et al. Molecular characterization of the major wheat domestication gene Q. Genetics 172, 547–555 (2006).
Komatsuda, T. et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc. Natl. Acad. Sci. USA 104, 1424–1429 (2007).
Li, C., Zhou, A. & Sang, T. Rice domestication by reducing shattering. Science 311, 1936–1939 (2006).
Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396 (2006).
Hong, S.K., Kitano, H., Satoh, H. & Nagato, Y. How is embryo size genetically regulated in rice? Development 122, 2051–2058 (1996).
Song, X.-J., Huang, W., Shi, M., Zhu, M.-Z. & Lin, H.-X.A. QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39, 623–630 (2007).
Isshiki, M. et al. Naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J. 15, 133–138 (1998).
Olesen, K.M. & Purugganan, M.D. Molecular evidence on the origin and evolution of glutinous rice. Genetics 162, 941–950 (2002).
Olsen, K.M. et al. Selection under domestication: evidence for a sweep in the rice Waxy genomic region. Genetics 173, 975–983 (2006).
Kojima, Y., Ebana, K., Fukuoka, S., Nagamine, T. & Kawase, M. Development of an RFLP-based rice diversity research set of germplasm. Breed. Sci. 55, 431–440 (2005).
Cheng, C. et al. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol. Biol. Evol. 20, 67–75 (2003).
Ma, J. & Bennetzen, J.L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101, 12404–12410 (2004).
Vitte, C., Ishii, T., Lamy, F., Brar, D. & Panaud, O. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol. Gen. Genet. 272, 504–511 (2004).
Ehrenreich, I.M. & Purugganan, M.D. The molecular genetic basis of plant adaptation. Am. J. Bot. 93, 953–962 (2006).
Acknowledgements
We thank H. Kanamori of Institute of the Society for Techno-Innovation of Agriculture, Forestry and Fisheries and T. Matsumoto of National Institute of Agrobiological Sciences for genomic sequencing of the qSW5 region of Kasalath, Y. Kojima for RFLP data production, and K. Ono for Kasalath transformation. M.Y. was supported by MP1113 (Integrated research project for plant, insect and animal using genome technology) and T.I. has been supported by GD2008 (Integrated research project for plant, insect and animal using genome technology) and QTL5001 (Genomics for Agricultural Innovation) of the Ministry of Agriculture, Forestry and Fisheries of Japan.
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A.S. performed most of the experiments. S.K. helped A.S. with the experiments and carried out qRT-PCR expression analysis. H.K. performed the original QTL analysis with the F2 population. T.E. field-tested NIL(qSW5). K.E. provided genome-wide RFLP data on rice landraces. M.Y. directed the QTL analysis, material production and fine mapping of qSW5. T.I. directed the research, designed the experiments for all the other parts and analyzed the FNPs with genome data, and wrote the manuscript. All authors contributed to improve the manuscript.
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Shomura, A., Izawa, T., Ebana, K. et al. Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40, 1023–1028 (2008). https://doi.org/10.1038/ng.169
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DOI: https://doi.org/10.1038/ng.169
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