Bai X. F., Zhao H., Huang Y., Xie W. B., Han Z. M., Zhang B., Guo Z. L., Yang L., Dong H. J., Xue W. Y., Li G. W., Hu G., Hu Y., and Xing Y. Z. (2016). Genome-wide association analysis reveals different genetic control in panicle architecture between Indica and Japonica rice. Plant Genome, 9(2): 1–10.
Barrett J. C., Fry B., Maller J., and Daly M. J. (2005). Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21: 263–265.
Chen W., Gao Y. Q., Xie W. B., Gong L., Lu K., Wang W. S., Li Y., Liu X. Q., Zhang H. Y., Dong H. X., Zhang W., Zhang L. J., Yu S. B., Wang G. W., Liang X. M., and Luo J. (2014). Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics, 46: 714–721.
Endo-Higashi N., and Izawa T. (2011). Flowering time genes Heading date 1 and Early heading date 1 together control panicle development in rice. Plant Cell Physiology, 52: 1083–1094.
Hori K., Ogiso-Tanaka E., Matsubara K., Yamanouchi U., Ebana K., and Yano M. (2013). Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant Journal, 76: 36–46.
Huang X. H., Kurata N., Wei X. H., Wang Z-X., Wang A. H., Zhao Q., Zhao Y., Liu K. Y., Lu H. Y., Li W. J., Guo Y. L., Lu Y. Q., Zhou C. C., Fan D. L., Weng Q. J., Zhu C. R., Huang T., Zhang L., Wang Y.C., Feng L., Furuumi H., Kubo T., Miyabayashi T., Yuan X. P., Xu Q., Dong G. J., Zhan Q. L., Li C. Y., Fujiyama A., Toyoda A., Lu T. T., Feng Q., Qian Q., Li J. Y., and Han B. (2012). A map of rice genome variation reveals the origin of cultivated rice. Nature, 490: 497–501.
Huang X. Z., Qian Q., Liu Z. B., Sun H. Y., He S. Y., Luo D., Xia G. M., Chu C. C., Li J. Y., and Fu, X. D. (2009). Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genetics, 41: 494–497.
Ikeda K., Nagasawa N., and Nagato Y. (2005). ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice. Developmental Biology, 282: 349–360.
Ikeda-Kawakatsu K., Maekawa M., Izawa T., Itoh J. I., and Nagato Y. (2012). ABERRANT PANICLE ORGANIZATION 2/RFL, the rice ortholog of Arabidopsis LEAFY, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1. Plant Journal, 69: 168–180.
Iwamoto M., and Takano M. (2011). Phytochrome-regulated EBL1 contributes to ACO1 upregulation in rice. Biotechnology Letters, 33: 173–178.
Li F., Liu W. B., Tang J. Y., Chen J. F., Tong H. N., Hu B., Li C. L., Fang J., Chen M. S., and Chu C. C. (2010). Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation. Cell Research, 20: 838–849.
Li M. X., Yeung J. M., Cherny S. S., and Sham P. C. (2012). Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Human Genetics, 131: 747–756.
Li S. B., Qian Q., Fu Z. M., Zeng D. L., Meng X. B., Kyozuka J., Maekawa M., Zhu X. D., Zhang J., Li J. Y., and Wang Y. H. (2009). Short panicle 1 encodes a putative PTR family transporter and determines rice panicle size. Plant Journal, 58: 592–605.
Li S. Y., Zhao B. R., Yuan D. Y., Duan M. J., Qian Q., Tang L., Wang B., Liu X. Q., Zhang J., Wang J., Sun J. Q., Liu Z., Feng Y. Q., Yuan L.P., and Li C. Y. (2013). Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression. Proceedings of the National Academy of Sciences USA, 110: 3167–3172.
Lippert C., Listgarten J., Liu Y., Kadie C. M., Davidson R. I., and Heckerman D. (2011). FaST linear mixed models for genome-wide association studies. Nature Methods, 8: 833–835.
Mather K. A., Caicedo A. L., Polato N. R., Olsen K. M., McCouch S., and Purugganan M. D. (2007). The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics, 177: 2223–2232.
McNally K. L., Childs K. L., Bohnert R., Davidson R. M., Zhao K., Ulat V. J., Zeller G., Clark R. M., Hoen D. R., Bureau T. E., Stokowski R., Ballinger D. G., Frazer K. A., Cox D. R., Padhukasahasram B., Bustamante C. D., Weigel D., Mackill D. J., Bruskiewich R. M., Rätsch G., Buell C. R., Leung H., and Leach J. E. (2009). Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences USA, 106: 12273–12278.
Oka H. I. (1988). Origin of cultivated rice. Japan Scientific Societies Press, Tokyo.
Piao R. H., Jiang W. Z., Ham T. H., Choi M. S., Qiao Y. L., Chu S. H., Park J. H., Woo M. O., Jin Z. X., An G., Lee J. Y., and Koh H. J. (2009). Map-based cloning of the ERECT PANICLE 3 gene in rice. Theoretical and Applied Genetics, 119: 1497–1506.
Qiao Y. L., Jiang W. Z., Lee J. H., Park B. S. Choi M-S., Piao R. H., Woo M-O., Roh J-H., Han L. Z., Paek N-C., Seo H. S., and Koh H-J. (2010). SPL28 encodes a clathrin-associated adaptor protein complex 1, medium subunit l1 (AP1M1) and is responsible for spotted leaf and early senescence in rice (Oryza sativa). New Phytologist, 185: 258–274.
Qiao Y. L., Piao R. H., Shi J. X., Lee S. I., Jiang W. Z., Kim B. K., Lee J. Y., Han L. Z., Ma W. B., and Koh H. J. (2011). Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.) Theoretical and Applied Genetics, 122: 1439–1449.
Rao N. N., Prasad K., Kumar P. R. and vijayraghavan U. (2008). Distinct regulatory role for RFL, the rice LFY homolog, in determining flowering time and plant architecture. Proceedings of the National Academy of Sciences USA, 105: 3646–3651.
Wang Q. X., Xie W. B., Xing H. K., Yan J., Meng Z. X., Li X. L., Fu X. K., Xu J. Y., Lian X. M., Yu S. B., Xing Y. Z., and Wang G. W. (2015). Genetic architecture of natural variation in rice chlorophyll content revealed by genome wide association study. Molecular Plant, 8: 946–957.
Wang Z. Y. and Tanksley S. D. (1989). Restriction fragment length polymorphism in Oryza sativa L.. Genome, 32: 1113–1118.
Xue W. Y., Xing Y. Z., Weng X. Y., Zhao Y., Tang W. J., Wang L., Zhou H. J., Yu S. B., Xu C. G., Li X. H., and Zhang Q. F. (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics,40: 761–767.
Yan W. H., Liu H. Y., Zhou X. C., Li Q. P., Zhang J., Lu L., Liu T. M., Liu H. J., Zhang C. J., Zhang Z. Y., Shen G. J., Yao W., Chen H. X., Yu S. B., Xie W. B., and Xing Y. Z. (2013). Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Research, 23: 969–971.
Yan W. H., Wang P., Chen H. X., Zhou H. J., Li Q. P., Wang C. R., Ding Z. H., Zhang Y. S., Yu S. B., Xing Y. Z., and Zhang Q. F. (2011). A Major QTL, Ghd8, Plays Pleiotropic Roles in Regulating Grain Productivity, Plant Height, and Heading Date in Rice. Molecular Plant,4: 319–330.
Yu J. M., Pressoir G., Briggs W. H., Bi I. V., Yamasaki M., Doebley J. F. McMullen M. D., Gaut B. S., Nielsen D. M., Holland J. B., Kresovich S., and Buckler E. S.(2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics,38: 203–208.
Zhang Q. F., Maroof M. A. S., Lu T. Y., and Shen B. Z. (1992). Genetic diversity and differentiation of Indica and Japonica rice detected by RFLP analysis. Theoretical and Applied Genetics, 83: 495–499.
Zhang Z. W., Ersoz E., Lai C. Q., Todhunter R. J., Tiwari H. K., Gore M. A., Bradbury P. J., Yu J., Arnett D. K., Ordovas J. M., and Buckler E. S. (2010). Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 42: 355–360.
Zhao K. Y., Tung C. W., Eizenga G. C., Wright M. H., Ali M. L., Price A. H., Norton G. J., Islam M. R., Reynolds A., Mezey J., McClung A. M., Bustamante C. D., and McCouch S. R. (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications, 2: 467.
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