Bewly JD. Seed germination and dormancy. Plant Cell. 1997;9:1055–66.
Li B, Foley ME. Genetic and molecular control of Seed Dormancy. Trends Plant Sci. 1997;2:384–9.
Baskin JM, Baskin CC. Classification system for seed dormancy. Seed Sci Res. 2004;14:1–16.
Baskin CC, Baskin JM. Seeds: ecology, biogeography, and evolution of dormancy and germination. San Diego: Academic; 1998.
Veasey EA, Karasawa MGM, Santos PP, Rosa MS, Mamanie E, Oliveira GCX. Variation in the loss of seed dormancy during after-ripening of wild and cultivated Rice Species. Ann Bot. 2004;94:875–82.
Harlan JR, de Wet JMJ, Price EG. Comparative evolution of cereals. Evolution. 1973;27:311–25.
Gubler F, Millar AA, Jacobsen JV. Dormancy release, ABA and pre-harvest sprouting. Curr Opin Plant Biol. 2005;8:183–7.
Bewley JD, Black M. Seeds- physiology of development and germination. 2nd ed. New York: Plenum Press; 1994.
Roberts EH. Dormancy of rice seed. I. The distribution of dormancy periods. J Exp Bot. 1961;13:319–39.
Roberts EH. Dormancy in rice seed. III. The influence of temperature, moisture and gaseous environment. J Exp Bot. 1962;13:75–94.
Anderson JA, Sorrells ME, Tanksley SD. RFLP analysis of genomic regions associated with resistance to pre-harvest sprouting in wheat. Crop Sci. 1993;33:453–9.
Ikehashi H. Induction and test of dormancy of rice seeds by temperature condition during maturation. Japan J Breed. 1972;22:209–16.
Takahashi N. Inheritance of seed germination and dormancy. In: Science of rice plant: genetics. Tokyo: Food and Agric Policy Res Center; 1997. p. 348–59.
Roberts EH. Dormancy in rice seed. IV. Varietal responses to storage and germination temperatures. J Exp Bot. 1965;16:341–9.
Cohn MA, Hughes JA. Seed dormancy in red rice (Oryza sativa). I. Effect of temperature on dry-afterripening. Weed Sci. 1981;29:402–4.
Koornneef M, Bentsink L, Hilhorst H. Seed dormancy and germination. Curr Opin Plant Biol. 2002;5:33–6.
Finkelstein RR. The role of hormones during seed development and Germination. In: Davies PJ, editor. Plant Hormones – biosynthesis, signal transduction, action! Dordrecht: The Netherlands: Kluwer Academic Publishers; 2004. p. 513–37.
Rohde A, Kurup S, Holdsworth M. ABI3 emerges from seed. Trends Plant Sci. 2000;5:418–9.
Monke G, Altschmied L, Tewes A, Reidt W, Mock HP, Baumlein H, et al. Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA. Planta. 2004;219:158–66.
Gualberti G, Papi M, Bellucci L, Ricci I, Bouchez D, Camilleri C, et al. Mutations in the Dof zinc finger genes DAG2 and DAG1 influence with opposite effects germination of Arabidopsis seeds. Plant Cell. 2002;14:1253–63.
Liu Y, Koornneef M, Soppe WJ. The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell. 2007;19:433–44.
Bentsink L, Jowett J, Hanhart CJ, Koornneef M. Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci U S A. 2006;103:17042–7.
Zheng J, Chen FY, Wang Z, Cao H, Li X, Deng X, et al. A novel role for histone methyltransferase KYP⁄SUVH4 in the control of Arabidopsis primary seed dormancy. New Phytol. 2012;193:605–16.
Xiang Y, Nakabayashi K, Ding J, He F, Bentsink L, Soppe WJJ. REDUCED DORMANCY5 Encodes a Protein Phosphatase 2C that Is Required for Seed Dormancy in Arabidopsis. Plant Cell. 2014;26:4362–75.
Footitt S, Müller K, Kermode AR, Finch-Savage WE. Seed dormancy cycling in Arabidopsis: chromatin remodeling and regulation of DOG1 in response to seasonal environmental signals. Plant J. 2015;81:413–25.
Gu XY, Foley ME, Horvath DP, Anderson JV, Feng J, Zhang L, et al. Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy Red rice. Genet. 2011;189:1515–24.
Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, et al. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A. 2010;107:5792–7.
Lin SY, Sasaki T, Yano M. Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theor Appl Genet. 1998;96:997–1003.
Dong Y, Tsuzuki E, Kamiunten H, Terao H, Lin D, Matsuo M, et al. Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice (Oryza sativa L.). Field crops Res. 2003;81:133–9.
Gu XY, Kianian SF, Foley ME. Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genet. 2004;166:1503–16.
Wan JM, Cao YJ, Wang CM, Ikehashi H. Quantitative trait loci associated with seed dormancy in rice. Crop Sci. 2005;45:712–6.
Jiang L, Cao YJ, Wang CM, Zhai HQ, Wan JM, Yoshimura A. Detection and analysis of QTL for seed dormancy in rice (Oryza sativa L.) using RIL and CSSL population. Acta Genet Sin. 2003;30:453–8.
Li W, Xu L, Bai X, Xing Y. Quantitative trait loci for seed dormancy in rice. Euphytica. 2010;178:427–35.
Gu XY, Turnipseed EB, Foley ME. The qSD12 locus controls offspring tissue-imposed seed dormancy in rice. Genet. 2008;179:2263–73.
Ye H, Beighley DH, Feng J, Gu XY. Genetic and physiological characterization of two clusters of quantitative trait loci associated with seed dormancy and plant height in rice. G3 (Bethesda). 2013;3:323–31.
Borevitz JO, Nordborg M. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 2003;132:718–25.
Korte A, Farlow A. The advantages and limitations of trait analysis with GWAS: a review. Plant Methods. 2013;9:29.
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009;106:9362–7.
Asimit J, Zeggini E. Rare variant association analysis methods for complex traits. Annu Rev Genet. 2010;44:293–308.
Gibson G. Rare and common variants: twenty arguments. Nat Rev Genet. 2011;13:135–45.
Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol. 2010;8(1):e1000294.
Wray NR, Purcell SM, Visscher PM. Synthetic associations created by rare variants do not explain most GWAS results. PLoS Biol. 2011;9(1):e1000579.
Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO. Association mapping of local climate sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010;107:21199–204.
Feng T, Zhu X. Detecting rare variants. Methods Mol Biol. 2012;850:453–64.
Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006;38:203–8.
Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, Heckerman D. Improved linear mixed models for genome-wide association studies. Nat Methods. 2012;9:525–6.
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010;42:961–7.
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in oryza sativa. Nat Commun. 2011;2:267. doi:10.1038/ncomms1467.
Norton GJ, Douglas A, Lahner B, Yakubova E, Guerinot ML, Pinson SRM, et al. Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One. 2014;9(2):e89685.
Eizenga GC, Ali ML, Bryant RJ, Yeater KM, McClung AM, McCouch SR. Registration of the ‘Rice Diversity Panel 1’ for genome-wide association studies. J Plant Registrations. 2014;8:109–16.
Yano R, Takebayashi Y, Nambara E, Kamiya Y, Seo M. Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. Plant J. 2013;74:815–28.
Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genet. 2007;177:2223–32.
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, et al. Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009;106:12273–8.
Ali-Rachedi S, Bouinot D, Wagner MH, Bonnet M, Sotta B, Grappin P, et al. Changes in endogenous abscisic acid levels during dormancy release and maintenance of mature seeds: studies with the Cape Verde Islands ecotype, the dormant model of Arabidopsis thaliana. Planta. 2004;219:479–88.
Cadman CS, Toorop PE, Hilhorst HW, Finch-Savage WE. Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. Plant J. 2006;46:805–22.
Sakai M, Sakamoto T, Saito T, Matsuoka M, Tanaka H, Kobayashi M. Expression of novel rice gibberellin 2-oxidase gene is under homeostatic regulation by biologically active gibberellins. J Plant Res. 2003;116:161–4.
Zhu Y, Nomura T, Xu Y, Zhang Y, Peng Y, Mao B, et al. Elongated uppermost internode encodes a cytochrome P450 monooxygenase that epoxidizes gibberellins in a novel deactivation reaction in rice. Plant Cell. 2006;18:442–56.
Luo A, Qian Q, Yin HF, Liu XQ, Yin CX, Lan Y, et al. EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin response in rice. Plant Cell Physiol. 2006;47:181–91.
Fu J, Liu H, Li Y, Yu H, Li X, Xiao J, et al. Manipulating broad-spectrum disease resistance by suppressing pathogen-induced auxin accumulation in rice. Plant Physiol. 2011;155:589–602.
Finkelstein R, Lynch T. The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell. 2000;12:599–609.
Gardner HW, Dornbos DLJ, Desjardins A. Hexanal, trans-2-hexenal, and trans-2-nonenal inhibit soybean, Glycine max, seed germination. J Agric Food Chem. 1990;38:1316–20.
Chehab EW, Raman G, Walley JW, Perea JV, Banu G, Theg S, et al. Rice HYDROPEROXIDE LYASES with unique expression patterns generate distinct aldehyde signatures in Arabidopsis. Plant Physiol. 2006;141:121–34.
Vaidyanathan R, Kuruvilla S, Thomas G. Characterization and expression pattern of an abscisic acid and osmotic stress responsive gene from rice. Plant Sci. 1998;140:21–30.
Ni J, Colowit P, Mackill D. Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci. 2002;42:601–7.
Glaszmann JC. Isozymes and classification of Asian rice varieties. Theor Appl Genet. 1987;74:21–30.
Zhang Q, Maroof M, Lu T, Shen B. Genetic diversity and differentiation of Indica and Japonica rice detected by RFLP analysis. Theor Appl Genet. 1992;83:495–9.
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. Genetic structure and diversity in Oryza sativa L. Genet. 2005;169:1631–8.
Alonso-Blanco C, Bentsink L, Hanhart CJ, Vries HBE, Koornneef M. Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana. Genet. 2003;164:711–29.
Carrera E, Holman T, Medhurst A, Dietrich D, Footitt S, Theodoulou FL, et al. Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. Plant J. 2008;53:214–24.
Ye H, Feng JH, Zhang LH, Zhang JF, Mispan MS, Cao ZQ, et al. Map-based cloning of seed dormancy1–2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice. Plant Physiol. 2015;169:2152–65.
Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, et al. OsSPL14 promotes panicle branching and higher productivity in rice. Nat Genet. 2010;42:545–50.
Gianinetti A, Vernier P. On the role of abscisic acid in seed dormancy of red rice. J Exp Bot. 2007;58:3449–62. 2007.
Gubler F, Hughes T, Waterhouse P, Jacobsen J. Regulation of dormancy in barley by blue light and after-ripening: effects on abscisic acid and gibberellin metabolism. Plant Physiol. 2008;147:886–96.
Rodriguez MV, Mendiondo GM, Cantoro R, Auge GA, Luna V, Masciarelli O, et al. Expression of seed dormancy in grain sorghum lines with contrasting pre-harvest sprouting behavior involves differential regulation of gibberellin metabolism genes. Plant Cell Physiol. 2012;53:64–80.
Chen W, Gao Y, Xie W, Gong L, Lu K, Wang W, et al. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet. 2014;46:714–21.
Zhao H, Yao W, Ouyang Y, Yang W, Gong W, Wang GW, et al. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res. 2014. 43 doi: 10.1093/nar/gku894.
Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D, et al. FaST linear mixed models for genome-wide association studies. Nat Methods. 2011;8:833–5.
Li MX, Yeung JM, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012;131:747–56.
Gu XY, Kianian SF, Foley ME. Phenotypic selection for seed dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice. Genet. 2005;171:695–704.
Cai HW, Morishima H. Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet. 2000;100:840–6.