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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.
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.
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.
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.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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