Ali F, Qanmber G, Li F, Wang Z. 2022. Updated role of ABA in seed maturation, dormancy, and germination. Journal of Advanced Research, 35, 199–214.

Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.

Bevan M W, Uauy C, Wulff B B H, Zhou J, Krasileva K, Clark M D. 2017. Genomic innovation for crop improvement. Nature, 543, 346–354.

Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2635.

Chen W, Wang W, Lyu Y, Wu Y, Huang P, Hu S, Wei X, Jiao G, Sheng Z, Tang S, Shao G, Luo J. 2021. OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway. The Crop Journal, 9, 68–78.

Danecek P, Auton A, Abecasis G, Albers C A, Banks E,  DePristo A M, Handsaker E R, Lunter G, Marth T G, Sherry T S, McVean G, Durbin R, 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.

Day P M. 2008. Phosphatidylinositol 3-kinase is a positive regulator of gibberellin signaling. Ph D thesis, The Pennsylvania State University, USA.

Deng X, An B, Zhong H, Yang J, Kong W, Li Y. 2019. A Novel insight into functional divergence of the MST gene family in rice based on comprehensive expression patterns. Genes, 10, 239.

Fernie A R, Gutierrez-Marcos J. 2019. From genome to phenome: Genome-wide association studies and other approaches that bridge the genotype to phenotype gap. The Plant Journal, 97, 5–7.

Finch-Savage W E, Leubner-Metzger G. 2006. Seed dormancy and the control of germination. New Phytologist, 171, 501–523.

Finkelstein R, Reeves W, Ariizumi T, Steber C. 2008. Molecular aspects of seed dormancy. Annual Review of Plant Biology, 59, 387–415.

Francis R M. 2017. Pophelper: An R package and web app to analyse and visualize population structure. Molecular Ecology Resources, 17, 27–32.

Fu K, Song W, Chen C, Mou C, Huang Y, Zhang F, Hao Q, Wang P, Ma T, Chen Y, Zhu Z. 2022. Improving pre-harvest sprouting resistance in rice by editing OsABA8ox using CRISPR/Cas9. Plant Cell Reports, 41, 2107–2110.

Gabriel S B, Schaffner S F, Nguyen H, Moore J M, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero S N. 2002. The structure of haplotype blocks in the human genome. Science, 296, 2225–2229.

Ge S X, Jung D, Yao R. 2020. ShinyGO: A graphical gene-set enrichment tool for animals and plants. Bioinformatics, 36, 2628–2629.

Gu X Y, Chen Z X, Foley M E. 2003. Inheritance of seed dormancy in weedy rice. Crop Science, 43, 835–843.

Haake V, Cook D, Riechmann J L, Pineda O, Thomashow M F, Zhang J Z. 2002. Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiology, 130, 639–648.

Hou M Y, Wang C M, Jiang L, Wan J M, Yasui H, Yoshimura A. 2004. Inheritance and QTL mapping of low temperature germinability in rice (Oryza sativa L.). Acta Genetica Sinica, 31, 701–706. (in Chinese)

Hu Y, Zhao L, Chong K, Wang T. 2008. Overexpression of OsERF1, a novel rice ERF gene, up-regulates ethylene-responsive genes expression besides affects growth and development in Arabidopsis. Journal of Plant Physiology, 165, 1717–1725.

Huang X, Kurata N, Wei X, Wang Z X, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature, 490, 497–501.

Jain M, Khurana J P. 2009. Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. The FEBS Journal, 276, 3148–3162.

Jang S G, Kim B, Choi I, Lee J, Ham T H, Kwon S W. 2023. Fine-mapping analysis of the genes associated with pre-harvest sprouting tolerance in rice (Oryza sativa L.). Agronomy, 13, 818.

Kermode A R, Bewley J D. 1989. Developing seeds of Ricinus communis L., when detached and maintained in an atmosphere of high relative humidity, switch to a germinative mode without the requirement for complete desiccation. Plant Physiology, 90, 702–707.

Kim K W, Chung H K, Cho G T, Ma K H, Chandrabalan D, Gwag J G, Kim T S, Cho E G, Park Y J. 2007. PowerCore: A program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics, 23, 2155–2162.

Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874.

Lan J, Lin Q, Zhou C, Ren Y, Liu X, Miao R, Jing R, Mou C, Nguyen T, Zhu X, Wang Q, Zhang X, Guo X, Liu S, Jiang L, Wan J. 2020. Small grain and semi-dwarf 3, a WRKY transcription factor, negatively regulates plant height and grain size by stabilizing SLR1 expression in rice. Plant Molecular Biology, 104, 429–450.

Lee G A, Jeon Y A, Lee H S, Hyun D Y, Lee J R, Lee M C, Lee S Y, Ma K H, Koh H J. 2017. New genetic loci associated with preharvest sprouting and its evaluation based on the model equation in rice. Frontiers in Plant Science, 8, 1393.

Lee G A, Jeon Y A, Lee H S, Hyun D Y, Lee J R, Lee M C, Lee S Y, Ma K H, Koh H J. 2018. Variation in pre-harvest sprouting resistance, seed germination and changes in abscisic acid levels during grain development in diverse rice genetic resources. Plant Genetic Resources, 16, 18–27.

Lee J, Kwon S W. 2015. Analysis of quantitative trait loci associated with seed germination and coleoptile length under low temperature condition. Journal of Crop Science and Biotechnology, 18, 273–278.

Lee J S, Chebotarov D, McNally K L, Pede V, Setiyono T D, Raquid R, Hyun W J, Jeung J U, Kohli A, Mo Y. 2021. Novel sources of pre-harvest sprouting resistance for japonica rice improvement. Plants, 10, 1709.

Leubner-Metzger G, Petruzzelli L, Waldvogel R, Vögeli-Lange R, Meins F. 1998. Ethylene-responsive element binding protein (EREBP) expression and the transcriptional regulation of class I β-1,3-glucanase during tobacco seed germination. Plant Molecular Biology, 38, 785–795.

Liang S, Xiong W, Yin C, Xie X, Jin Y J, Zhang S, Yang B, Ye G, Chen S, Luan W J. 2019. Overexpression of OsARD1 improves submergence, drought, and salt tolerances of seedling through the enhancement of ethylene synthesis in rice. Frontiers in Plant Science, 10, 1088.

Licausi F, Ohme-Takagi M, Perata P. 2013. APETALA2/ethylene responsive factor (AP2/ERF) transcription factors: Mediators of stress responses and developmental programs. The New Phytologist, 199, 639–649.

Lipka A E, Tian F, Wang Q, Peiffer J, Li M, Bradbury P J, Gore M A, Buckler E S, Zhang Z. 2012. GAPIT: Genome association and prediction integrated tool. Bioinformatics, 28, 2397–2399.

Liu L, Xia W, Li H, Zeng H, Wei B, Han S, Yin C. 2018. Salinity inhibits rice seed germination by reducing α-amylase activity via decreased bioactive gibberellin content. Frontiers in Plant Science, 9, 275.

Liu J, Zhou J, Xing D. 2012. Phosphatidylinositol 3-kinase plays a vital role in regulation of rice seed vigor via altering NADPH oxidase activity. PLoS ONE, 7, e33817.

Lo S F, Yang S Y, Chen K T, Hsing Y I, Zeevaart J A D, Chen L J, Yu S M. 2008. A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice. The Plant Cell, 20, 2603–2618.

Lorenzo O, Piqueras R, Sánchez-Serrano J J, Solano R. 2003. ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. The Plant Cell, 15, 165–178.

Lu Q, Niu X, Zhang M, Wang C, Xu Q, Feng Y, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Chen X, Liang X, Wei X. 2018. Genome-wide association study of seed dormancy and the genomic consequences of improvement footprints in rice (Oryza sativa L.). Frontiers in Plant Science, 8, 2213.

Lu Q, Zhang M, Niu X, Wang S, Xu Q, Feng Y, Wang C, Deng H, Yuan X, Yu H, Wang Y, Wei X. 2015. Genetic variation and association mapping for 12 agronomic traits in indica rice. BMC Genomics, 16, 1067.

Magwa R A, Zhao H, Xing Y. 2016. Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.). BMC Genetics, 17, 28.

Mather K A, Caicedo A L, Polato N R, Olsen K M, McCouch S, Purugganan M D. 2007. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics, 177, 2223–2232.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.

Miao C, Wang Z, Zhang L, Yao J, Hua K, Liu X, Shi H, Zhu J K. 2019. The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice. Nature Communication, 10, 3822.

Miyamoto T, Takada R, Tobimatsu Y, Suzuki S, Yamamura M, Osakabe K, Osakabe Y, Sakamoto M, Umezawa T. 2020. Double knockout of OsWRKY36 and OsWRKY102 boosts lignification with altering culm morphology of rice. Plant Science, 296, 110466.

Mohanty B, Takahashi H, de Los Reyes B G, Wijaya E, Nakazono M, Lee D Y. 2016. Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence. Rice, 9, 51.

Müller M, Munné-Bosch S. 2015. Ethylene response factors: A key regulatory hub in hormone and stress signaling. Plant Physiology, 169, 32–41.

Nonogaki H, Barrero J M, Li C. 2018. Editorial: Seed dormancy, germination, and pre-harvest sprouting. Frontiers in Plant Science, 9, 1783.

Nonogaki M, Nonogaki H. 2017. Prevention of preharvest sprouting through hormone engineering and germination recovery by chemical biology. Frontiers in Plant Science, 8, 90.

Oracz K, El-Maarouf-Bouteau H, Bogatek R, Corbineau F, Bailly C. 2008. Release of sunflower seed dormancy by cyanide: Cross-talk with ethylene signalling pathway. Journal of Experimental Botany, 59, 2241–2251.

Park M, Choi W, Shin S Y, Moon H, Lee D, Gho Y S, Jung K H, Jeon J S, Shin C. 2021. Identification of genes and microRNAs affecting pre-harvest sprouting in rice (Oryza sativa L.) by transcriptome and small RNAome analyses. Frontiers in Plant Science, 12, 1677.

Phitaktansakul R, Kim K W, Aung K M, Maung T Z, Min M H, Somsri A, Lee W, Lee S B, Nam J, Kim S H, Lee J, Kwon S K, Nawade B, Chu S H, Park S W, Kang K K, Cho Y H, Lee Y S, Chung I M, Park Y J. 2022. Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2. Journal of Advanced Research, 42, 303–314.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, De Bakker P I, Daly M J. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559–575.

Raj A, Stephens M, Pritchard J K. 2014. fastSTRUCTURE: Variational inference of population structure in large SNP data sets. Genetics, 197, 573–589.

Rashid M, He G Y, Yang G X, Hussain J, Yan X. 2012. AP2/ERF transcription factor in rice: Genome-wide canvas and syntenic relationships between monocots and eudicots. Evolutionary Bioinformatics, 8, 321–355.

Rodríguez M V, Barrero J M, Corbineau F, Gubler F, Benech-Arnold R L. 2015. Dormancy in cereals (not too much, not so little): About the mechanisms behind this trait. Seed Science Research, 25, 99–119.

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, Guirao-Rico S, Librado P, Ramos-Onsins S E, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34, 3299–3302.

Shu K, Meng Y J, Shuai H W, Liu W G, Du J B, Liu J, Yang W Y. 2015. Dormancy and germination: How does the crop seed decide? Plant Biology, 17, 1104–1112.

Sohn S I, Pandian S, Kumar T S, Zoclanclounon Y A B, Muthuramalingam P, Shilpha J, Satish L, Ramesh M. 2021. Seed dormancy and pre-harvest sprouting in rice - An updated overview. International Journal of Molecular Sciences, 22, 11804.

Song S, Wang G, Wu H, Fan H, Liang L, Zhao H, Li S, Hu Y, Liu H, Ayyad M, Xing Y, 2020. OsMFT2 is involved in the regulation of ABA signaling-mediated seed germination through interacting with OsbZIP23/66/72 in rice. The Plant Journal, 103, 532–546.

Stagnati L, Lanubile A, Samayoa L F, Bragalanti M, Giorni P, Busconi M, Holland J B, Marocco A. 2019. A genome-wide association study reveals markers and genes associated with resistance to Fusarium verticillioides infection of seedlings in a maize diversity panel. G3, 9, 571–579.

Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M. 2010. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences of the United States of America, 107, 5792–5797.

Sweeney M T, Thomson M J, Pfeil B E, McCouch S. 2006. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. The Plant Cell, 18, 283–294.

Tai L, Wang H J, Xu X J, Sun W H, Ju L, Liu W T, Li W Q, Sun J, Chen K M. 2021. Pre-harvest sprouting in cereals: Genetic and biochemical mechanisms. Journal of Experimental Botany, 72, 2857–2876.

Toolkit P. 2019. Broad institute, GitHub repository. [2022-12-22]. http://broadinstitute.github.io/picard

Upadhyaya H D, Wang Y H, Sastry D V, Dwivedi S L, Prasad P V, Burrell A M, Klein R R, Morris G P, Klein P E. 2016. Association mapping of germinability and seedling vigor in sorghum under controlled low-temperature conditions. Genome, 59, 137–145.

Varshney R K, Bohra A, Yu J, Graner A, Zhang Q, Sorrells M E. 2021. Designing future crops: Genomics-assisted breeding comes of age. Trends in Plant Science, 26, 631–649.

Wang H, Zhang Y, Xiao N, Zhang G, Wang F, Chen X, Fang R. 2020. Rice GERMIN-LIKE PROTEIN 2–1 functions in seed dormancy under the control of abscisic acid and gibberellic acid signaling pathways. Plant Physiology, 183, 1157–1170.

Wickham H, Chang W, Wickham M H. 2016. Package ‘ggplot2’. Create elegant data visualisations using the grammar of graphics. Version, 2, 1–189.

Wilson R L, Kim H, Bakshi A, Binder B M. 2014. The ethylene receptors ETHYLENE RESPONSE1 and ETHYLENE RESPONSE2 have contrasting roles in seed germination of Arabidopsis during salt stress. Plant Physiology, 165, 1353–1366.

Wing R A, Purugganan M D, Zhang Q. 2018. The rice genome revolution: From an ancient grain to Green Super Rice. Nature Reviews Genetics, 19, 505–517.

Xu F, Tang J, Gao S, Cheng X, Du L, Chu C. 2019. Control of rice pre-harvest sprouting by glutaredoxin-mediated abscisic acid signaling. Plant Journal, 100, 1036–1051.

Xu F, Tang J, Wang S, Cheng X, Wang H, Ou S, Gao S, Li B, Qian Y, Gao C, Chu C. 2022. Antagonistic control of seed dormancy in rice by two bHLH transcription factors. Nature Genetics, 54, 1972–1982.

Xu H, Gao Y, Wang J. 2012. Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PLoS ONE, 7, e30646.

Xu S, Wang L, Zhang B, Han B, Xie Y, Yang J, Zhong W, Chen H, Wang R, Wang N, Cui W, Shen W. 2012. RNAi knockdown of rice SE5 gene is sensitive to the herbicide methyl viologen by the down-regulation of antioxidant defense. Plant Molecular Biology, 80, 219–235.

Yang C, Lu X, Ma B, Chen S Y, Zhang J S. 2015. Ethylene signaling in rice and Arabidopsis: Conserved and diverged aspects. Molecular Plant, 8, 495–505.

Yang J, Lee S H, Goddard M E, Visscher P M. 2011. GCTA: A tool for genome-wide complex trait analysis. American Journal of Human Genetics, 88, 76–82.

Zhang C, Zhou L, Lu Y, Yang Y, Feng L, Hao W, Li Q, Fan X, Zhao D, Liu Q. 2020. Changes in the physicochemical properties and starch structures of rice grains upon pre-harvest sprouting. Carbohydrate Polymers, 234, 115893.

Zhang Z, 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, Buckler E S. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 42, 355–360.

Zhao B, Zhang H, Chen T, Ding L, Zhang L, Ding X, Zhang J, Qian Q, Xiang Y. 2022. Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice. Journal of Integrative Plant Biology, 64, 1246–1263.

Zhao H, Li J, Yang L, Qin G, Xia C, Xu X, Su Y, Liu Y, Ming L, Chen L L, Xiong L, Xie W. 2021. An inferred functional impact map of genetic variants in rice. Molecular Plant, 14, 1584–1599.

Zhou C, Lin Q, Lan J, Zhang T, Liu X, Miao R, Mou C, Nguyen T, Wang J, Zhang X, Zhou L, Zhu X, Wang Q, Zhang X, Guo X, Liu S, Jiang L, Wan J. 2020. WRKY transcription factor OsWRKY29 represses seed dormancy in rice by weakening abscisic acid response. Frontiers Plant Science, 11, 691.

Zhou Q, Wang Q, Ye S, Cui M, Lei W, Gao H, Zhao Y, Xu X, Tang Z, Li J, Cui C. 2019. Genome-wide association analysis of tribenuron-methyl tolerance related traits in Brassica napus L. under germination. Scientia Agricultura Sinica, 5, 399–413. (in Chinese)

Zhu D, Qian Z, Wei H, Guo B, Xu K, Dai Q, Zhang H, Huo Z. 2019. The effects of field pre-harvest sprouting on the morphological structure and physicochemical properties of rice (Oryza sativa L.) starch. Food Chemistry, 278, 10–16.