Publications

Ando T, Yamamoto T, Shimizu T, Ma XF, et al. (2008). Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor. Appl. Genet. 116: 881-890. http://dx.doi.org/10.1007/s00122-008-0722-6 PMid:18274726   Ashikari M, Sakakibara H, Lin S, Yamamoto T, et al. (2005). Cytokinin oxidase regulates rice grain production. Science 309: 741-745. http://dx.doi.org/10.1126/science.1113373 PMid:15976269   Clark RM (2010). Genome-wide association studies coming of age in rice. Nat. Genet. 42: 926-927. http://dx.doi.org/10.1038/ng1110-926 PMid:20980987   Collins FS (1995). Positional cloning moves from perditional to traditional. Nat. Genet. 9: 347-350. http://dx.doi.org/10.1038/ng0495-347 PMid:7795639   Doi K, Izawa T, Fuse T, Yamanouchi U, et al. (2004). Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 18: 926-936. http://dx.doi.org/10.1101/gad.1189604 PMid:15078816 PMCid:395851   Fukuoka S and Saka N (2006). Marker assisted combination of QTLs for yield resistance blast in rice. Breed. Res. 8: 191.   Gilchrist EJ, Haughn GW, Ying CC, Otto SP, et al. (2006). Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol. Ecol. 15: 1367-1378. http://dx.doi.org/10.1111/j.1365-294X.2006.02885.x PMid:16626459   Gore MA, Chia JM, Elshire RJ, Sun Q, et al. (2009). A first-generation haplotype map of maize. Science 326: 1115-1117. http://dx.doi.org/10.1126/science.1177837 PMid:19965431   Hadiarto T and Tran LS (2011). Progress studies of drought-responsive genes in rice. Plant Cell Rep. 30: 297-310. http://dx.doi.org/10.1007/s00299-010-0956-z PMid:21132431   Han B, Xue Y, Li J, Deng XW, et al. (2007). Rice functional genomics research in China. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362: 1009-1021. http://dx.doi.org/10.1098/rstb.2007.2030 PMid:17347106 PMCid:2435567   Hao W and Lin HX (2010). Toward understanding genetic mechanisms of complex traits in rice. J. Genet. Genomics 37: 653-666. http://dx.doi.org/10.1016/S1673-8527(09)60084-9   Hu KM, Qiu DY, Shen XL, Li XH, et al. (2008). Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach. Mol. Plant 1: 786-793. http://dx.doi.org/10.1093/mp/ssn039 PMid:19825581   Huang X, Feng Q, Qian Q, Zhao Q, et al. (2009). High-throughput genotyping by whole-genome resequencing. Genome Res. 19: 1068-1076. http://dx.doi.org/10.1101/gr.089516.108 PMid:19420380 PMCid:2694477   Huang X, Wei X, Sang T, Zhao Q, et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42: 961-967. http://dx.doi.org/10.1038/ng.695 PMid:20972439   International Rice Genome Sequencing Project (IRGSP) (2005). The map-based sequence of the rice genome. Nature 436: 793-800. http://dx.doi.org/10.1038/nature03895 PMid:16100779   Ito Y, Katsura K, Maruyama K, Taji T, et al. (2006). Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol. 47: 141-153. http://dx.doi.org/10.1093/pcp/pci230 PMid:16284406   Li X, Qian Q, Fu Z, Wang Y, et al. (2003). Control of tillering in rice. Nature 422: 618-621. http://dx.doi.org/10.1038/nature01518 PMid:12687001   Lin HX, Yamamoto T, Sasaki T and Yano M (2000). Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor. Appl. Genet. 101: 1021-1028. http://dx.doi.org/10.1007/s001220051576   Londo JP, Chiang YC, Hung KH, Chiang TY, et al. (2006). Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc. Natl. Acad. Sci. U. S. A. 103: 9578-9583. http://dx.doi.org/10.1073/pnas.0603152103 PMid:16766658 PMCid:1480449   Manosalva PM, Davidson RM, Liu B, Zhu X, et al. (2009). A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiol. 149: 286-296. http://dx.doi.org/10.1104/pp.108.128348 PMid:19011003 PMCid:2613727   McCouch SR, Zhao K, Wright M, Tung CW, et al. (2010). Development of genome-wide SNP assays for rice. Breed. Sci. 60: 524-535. http://dx.doi.org/10.1270/jsbbs.60.524   Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, et al. (2008). Allelic diversification at the wx locus in landraces of Asian rice. Theor. Appl. Genet. 116: 979-989. http://dx.doi.org/10.1007/s00122-008-0729-z PMid:18305920   Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, et al. (2004). Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167: 1361-1369. http://dx.doi.org/10.1534/genetics.103.024950 PMid:15280248 PMCid:1470957   Ookawa T, Hobo T, Yano M, Murata K, et al. (2010). New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat. Commun. 1: 132. http://dx.doi.org/10.1038/ncomms1132 PMid:21119645 PMCid:3065348   Peltonen L, Palotie A and Lange K (2000). Use of population isolates for mapping complex traits. Nat. Rev. Genet. 1: 182-190. http://dx.doi.org/10.1038/35042049 PMid:11252747   Rabbani MA, Maruyama K, Abe H, Khan MA, et al. (2003). Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol. 133: 1755-1767. http://dx.doi.org/10.1104/pp.103.025742 PMid:14645724 PMCid:300730   Rafalski JA (2010). Association genetics in crop improvement. Curr. Opin. Plant Biol. 13: 174-180. http://dx.doi.org/10.1016/j.pbi.2009.12.004 PMid:20089441   Ren ZH, Gao JP, Li LG, Cai XL, et al. (2005). A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat. Genet. 37: 1141-1146. http://dx.doi.org/10.1038/ng1643 PMid:16155566   Sasaki T (2003). Rice genome analysis: understanding the genetic secrets of the rice plant. Breed. Sci. 53: 281-289. http://dx.doi.org/10.1270/jsbbs.53.281   Steele KA, Edwards G, Zhu J and Witcombe JR (2004). Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding. Theor. Appl. Genet. 109: 1247-1260. http://dx.doi.org/10.1007/s00122-004-1732-7 PMid:15300383   Takeda T, Suwa Y, Suzuki M, Kitano H, et al. (2003). The OsTB1 gene negatively regulates lateral branching in rice. Plant J. 33: 513-520. http://dx.doi.org/10.1046/j.1365-313X.2003.01648.x PMid:12581309   Takeuchi Y, Ebitani T, Yamamoto T, Sato H, et al. (2006). Development of isogenic lines of rice cultivar Koshihikari with early and late heading by marker-assisted selection. Breed. Sci. 56: 405-413. http://dx.doi.org/10.1270/jsbbs.56.405   Tian Z, Qian Q, Liu Q, Yan M, et al. (2009). Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc. Natl. Acad. Sci. U. S. A. 106: 21760-21765. http://dx.doi.org/10.1073/pnas.0912396106 PMid:20018713 PMCid:2793318   Wang LQ, Liu WJ, Xu Y, He YQ, et al. (2007). Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor. Appl. Genet. 115: 463-476. http://dx.doi.org/10.1007/s00122-007-0580-7 PMid:17593343   Xiang Y, Tang N, Du H, Ye H, et al. (2008). Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol. 148: 1938-1952. http://dx.doi.org/10.1104/pp.108.128199 PMid:18931143 PMCid:2593664   Xie W, Feng Q, Yu H, Huang X, et al. (2010). Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. U. S. A. 107: 10578-10583. http://dx.doi.org/10.1073/pnas.1005931107 PMid:20498060 PMCid:2890813   Xing Y and Zhang Q (2010). Genetic and molecular bases of rice yield. Annu. Rev. Plant Biol. 61: 421-442. http://dx.doi.org/10.1146/annurev-arplant-042809-112209 PMid:20192739   Xu K, Xu X, Fukao T, Canlas P, et al. (2006). Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705-708. http://dx.doi.org/10.1038/nature04920 PMid:16900200   Xu X, Liu X, Ge S, Jensen JD, et al. (2012). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30: 105-111. http://dx.doi.org/10.1038/nbt.2050 PMid:22158310   Yano M and Sasaki T (1997). Genetic and molecular dissection of quantitative traits in rice. Plant Mol. Biol. 35: 145-153. http://dx.doi.org/10.1023/A:1005764209331 PMid:9291968   Zhang Q, Li J, Xue Y, Han B, et al. (2008). Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol. Plant 1: 715-719. http://dx.doi.org/10.1093/mp/ssn043 PMid:19825575