Chinese Journal OF Rice Science >
Bioinformatics Analysis, Development and Application of Molecular Markers for Seed Dormancy Gene Sdr4 in Rice
Received date: 2025-02-25
Revised date: 2025-03-21
Online published: 2026-01-21
【Objective】Pre-harvest sprouting (PHS) severely compromises rice yield and grain quality, which is strongly influenced by seed dormancy genes. This study aims to elucidate the biological function of the seed dormancy gene Sdr4 and develop molecular markers for germplasm improvement, providing theoretical and practical insights for PHS-resistant rice breeding.【Method】A combination of bioinformatics analysis, molecular marker development, and marker-assisted selection was employed to systematically investigate Sdr4 functionality. Allelic variations between the strong-dormancy accession Kasalath and the weak-dormancy accession Nipponbare were analyzed to design genotype-specific markers.【Result】The Sdr4 promoter harbors core regulatory elements (e.g., TATA-box) and ABA-responsive cis-elements. The encoded protein is hydrophobic, exhibits low stability, and is extensively phosphorylated (25.93% within amino acids 101-150). Tertiary structure prediction indicated a composition of 15.50% α-helices, 15.50% β-sheets, and 66.37% random coils. Haplotype analysis of the 3K Rice Genome panel combined with AlphaFold modeling revealed that Sdr4 comprises six functional mutation-associated haplotypes. Furthermore, multiple amino acid sequence differences were identified in the Sdr4 protein between Kasalath and Nipponbare. Phylogenetic analysis demonstrated high conservation with Oryza glaberrima and Zizania palustris. Two functional markers (Sdr4-KF/KR and Sdr4-PF/PR) were developed to discriminate dormancy strength, and their efficacy was validated across 25 rice cultivars. Application of these markers in improving Zhongzhu 18 successfully generated novel lines with enhanced seed dormancy.【Conclusion】Sdr4 plays a critical role in regulating PHS resistance through the modulation of seed dormancy. Molecular screening confirmed weak dormancy phenotypes in 20 commercial varieties. The improved lines K17 and K88, developed via Sdr4-specific markers, exhibited significantly enhanced PHS resistance. This study establishes a framework for Sdr4 functional analysis and accelerates the molecular breeding of PHS-resistant rice germplasm.
HUANG Qina, JIANG Hongrui, YANG Jie, YU Kunyu, YANG Changdeng, LIANG Yan . Bioinformatics Analysis, Development and Application of Molecular Markers for Seed Dormancy Gene Sdr4 in Rice[J]. Chinese Journal OF Rice Science, 2026 , 40(1) : 61 -71 . DOI: 10.16819/j.1001-7216.2026.250211
| [1] | Finch-savage W E, Leubner-metzger G. Seed dormancy and the control of germination[J]. New Phytologist, 2006, 171: 501-523. |
| [2] | Sohn S I, Pandian S, Kumar T S, Zoclanclounon Y A B, Muthuramalingam P, Shilpha J, Satish L, Ramesh M. Seed dormancy and pre-harvest sprouting in rice: An updated overview[J]. International Journal of Molecular Sciences, 2021, 22(21): 11804. |
| [3] | Finkelstein R, Reeves W, Ariizumi T, Steber C. Molecular aspects of seed dormancy[J]. Annual Review of Plant Biology, 2008, 59: 387-415. |
| [4] | Chen W, Wang W, Lyu Y, Wu Y, Huang P, Hu S, Wei X, Jiao G, Sheng Z, Tang S, Shao G, Luo J. OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway[J]. The Crop Journal, 2021, 9: 68-78. |
| [5] | He D, Yang P. Proteomics of rice seed germination[J]. Frontiers in Plant Science, 2013, 4: 246. |
| [6] | Liu S, Sehgal S K, Li J, Lin M, Trick H N, Yu J, Gill B S, Bai G. Cloning and characterization of a critical regulator for preharvest sprouting in wheat[J]. Genetics, 2013, 195(1): 263-273. |
| [7] | Shu K, Meng Y J, Shuai H W, Liu W G, Du J B, Liu J, Yang W Y. Dormancy and germination: How does the crop seed decide?[J]. Plant Biology, 2015, 17(6): 1104-1112. |
| [8] | Falade K O, Semon O M, Fadairo O S, Oladunjoye A O, Orou K K. Functional and physico-chemical properties of flours and starches of African rice cultivars[J]. Food Hydrocolloids, 2014, 39: 41-50. |
| [9] | Lee H S, Choi M G, Hwang W H, Jeong J H, Lee C G. Occurrence of rice preharvest sprouting varies greatly depending on past weather conditions during grain filling[J]. Field Crops Research, 2021, 264: 108087. |
| [10] | 胡伟民, 马华升, 樊龙江, 阮松林. 杂交水稻制种不育系穗上发芽特性[J]. 作物学报, 2003, 29(3): 441-446. |
| Hu W M, Ma H S, Fan L J, Ruan S L. Characteristics of pre-harvest sprouting in sterile lines in hybrid rice seeds production[J]. Acta Agronomica Sinica, 2003, 29(3): 441-446. (in Chinese with English abstract) | |
| [11] | Liao Y, Bai Q, Xu P, Wu T, Guo D, Peng Y, Zhang H, Deng X, Chen X, Luo M, Ali A, Wang W, Wu X. Mutation in rice abscisic Acid2 results in cell death, enhanced disease-resistance, altered seed dormancy and development[J]. Frontiers in Plant Science, 2018, 9: 405. |
| [12] | Nakamura S, Abe F, Kawahigashi H, Nakazono K, Tagiri A, Matsumoto T, Utsugi S, Ogawa T, Handa H, Ishida H, Mori M, Kawaura K, Ogihara Y, Miura H. A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination[J]. Plant Cell, 2011, 23(9): 3215-3229. |
| [13] | Nakamura S, Pourkheirandish M, Morishige H, Kubo Y, Nakamura M, Ichimura K, Seo S, Kanamori H, Wu J, Ando T, Hensel G, Sameri M, Stein N, Sato K, Matsumoto T, Yano M, Komatsuda T. Mitogen-activated protein Kinase Kinase 3 regulates seed dormancy in barley[J]. Current Biology, 2016, 26(6): 775-781. |
| [14] | Sato K, Yamane M, Yamaji N, Kanamori H, Tagiri A, Schwerdt J G, Fincher G B, Matsumoto T, Takeda K, Komatsuda T. Alanine aminotransferase controls seed dormancy in barley[J]. Nature Communications, 2016, 7: 11625. |
| [15] | Bentsink L, Jowett J, Hanhart C J, Koornneef M. Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(45): 17042-17047. |
| [16] | Cao H, Han Y, Li J, Ding M, Li Y, Li X, Chen F, Soppe W J, Liu Y. Arabidopsis thaliana SEED DORMAN-CY 4-LIKE regulates dormancy and germination by mediating the gibberellin pathway[J]. Journal of Experimental Botany, 2020, 71(3): 919-933. |
| [17] | Carrillo-barral N, Rodríguez-gacio M D C, Matilla A J. Delay of germination-1 (DOG1): A key to understanding seed dormancy[J]. Plants (Basel), 2020, 9(4): 480. |
| [18] | Liu F, Zhang H, Ding L, Soppe W J J, Xiang Y. RE-VERSAL OF RDO5 1, a homolog of rice seed dormancy4, interacts with bHLH57 and controls ABA biosynthesis and seed dormancy in Arabidopsis[J]. Plant Cell, 2020, 32(6): 1933-1948. |
| [19] | Hattori T, Terada T, Hamasuna S T. Sequence and functional analyses of the rice gene homologous to the maize Vp1[J]. Plant Molecular Biology, 1994, 24: 805-810. |
| [20] | Zhao B, Zhang H, Chen T, Ding L, Zhang L, Ding X, Zhang J, Qian Q, Xiang Y. Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice[J]. Journal of Integrative Plant Biology, 2022, 64(6): 1246-1263. |
| [21] | Fan X, Gao F, Liu Y, Huang W, Yang Y, Luo Z, Zhang J, Qi F, Lü J, Su X, Wang L, Song S, Ren G, Xing Y. The transcription factor CCT30 promotes rice preharvest sprouting by regulating sugar signalling to inhibit the ABA-mediated pathway[J]. Plant Biotechnology Journal, 2025, 23(2): 579-591. |
| [22] | Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(13): 5792-5797. |
| [23] | Du L, Xu F, Fang J, Gao S, Tang J, Fang S, Wang H, Tong H, Zhang F, Chu J, Wang G, Chu C. Endosperm sugar accumulation caused by mutation of PHS8/ ISA1 leads to pre-harvest sprouting in rice[J]. Plant Journal, 2018, 95(3): 545-556. |
| [24] | Magwa R A, Zhao H, Xing Y. Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)[J]. BMC Genetics, 2016, 17: 1-13. |
| [25] | Meyer R S, Purugganan M D. Evolution of crop species: Genetics of domestication and diversification[J]. Nature Reviews Genetics, 2013, 14(12): 840-852. |
| [26] | Edwards K, Johnstone C, Thompson C. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis[J]. Nucleic Acids Research, 1991, 19(6): 1349. |
| [27] | Hilhorst H W M, Karssen C M. Seed dormancy and germination: The role of abscisic acid and gibberellins and the importance of hormone mutants[J]. Plant Growth Regulation, 1992, 11: 225-238. |
| [28] | Omoarelojie L O, Kulkarni M G, Finnie J F, van Staden J. Smoke-derived cues in the regulation of seed germination: Are Ca2+-dependent signals involved?[J]. Plant Growth Regulation, 2022, 97(2): 343-355. |
| [29] | 张毛宁. 基于花生RIL群体的鲜种子发芽性状QTL定位及分子标记开发[D]. 郑州: 郑州大学, 2022. |
| Zhang M N. QTL mapping for fresh seed germination traits based on a peanut RIL population and molecular marker development[D]. Zhengzhou: Zhengzhou University, 2022. (in Chinese with English abstract) |
/
| 〈 |
|
〉 |