水稻粒型突变体sgd13的鉴定及其基因定位

doi:10.3864/j.issn.0578-1752.2025.24.001

Abstract

Abstract:

【Objective】Grain shape is an important agronomic trait affecting rice yield and quality, and its development is regulated by the three-dimensional morphology of grain (grain length, grain width, grain thickness). Identification and cloning of grain shape regulatory genes can enrich the molecular mechanism of rice grain development regulation, and provide theoretical basis and genetic resources for high-yield molecular design breeding of rice. 【Method】A stable inherited grain type mutant sgd13 (small grain and dwarf 13) was screened from the mutant library of Nanjing 9108 induced by ethyl methane sulfonate (EMS). The grain morphology, 1000-grain weight, seed setting rate, yield per plant, plant height, panicle length and other phenotypes of the mutants were statistically analyzed. Paraffin sections and scanning electron microscopy were used to analyze the changes in the number and size of glume and stem cells. The genetic analysis of sgd13 and Nanjing 9108 was carried out. The F₂ population constructed by sgd13 and Nanjing 9108 was used to locate the gene by BSA-seq technology. The SWISS-MODEL website was used to predict the three-dimensional structure of wild-type and mutant proteins. 【Result】The grains of sgd13 were significantly smaller and narrower, the grain length decreased by 19.98%, and the grain width decreased by 7.81%. Compared with WT, the plant height, spike length and yield per plant of sgd13 were significantly reduced. There was no significant difference in the number of internodes between sgd13 and WT, but the lengths of the first, second, third and sixth internodes were shorter. Cytological analysis showed that the glume and stem cells of sgd13 became smaller and less, indicating that sgd13 may affect organ development by regulating cell division and expansion. Genetic analysis confirmed that the trait was controlled by a single recessive nuclear gene. The candidate gene was mapped to LOC_Os01g52550 by BSA-seq, which encodes an ATP-binding cassette (ABC) transporter. The ABC transporter contains two typical core domains: A highly conserved nucleotide binding domain (NBD) and a less conserved transmembrane domain (TMD). In the sgd13 mutant, a single base substitution (T→A) occurred in the exon region of the gene, which was located in the NBD domain. This single base substitution directly causes the encoded amino acid to change from glutamic acid (E) to aspartic acid (D). Due to the differences in side chain structure and chemical properties between glutamic acid and aspartic acid, this change is likely to affect the spatial structure of SGD13 protein, thereby interfering with its normal function, and ultimately leading to a unique phenotype of the mutant sgd13. Genetic complementation experiments showed that the introduction of wild-type LOC_Os01g52550 could restore the grain shape of sgd13 to the wild-type level.【Conclusion】The sgd13 mutant phenotype was controlled by a single recessive nuclear gene, which was caused by the LOC_Os01g52550 mutation. The T→A mutation in the exon region of the gene causes the glutamic acid in the NBD domain to become aspartic acid, which affects the three-dimensional structure of the protein.

Key words: rice (Oryza sativa L.), grain shape, mutant, gene mapping, ABC transporter protein

ZHUANG LiHua, LUO Lei, ZHAO ChunFang, WANG JiZhong, ZHANG YaDong, HE Lei. Identification and Gene Mapping of Rice Grain Shape Mutant sgd13[J].Scientia Agricultura Sinica, 2025, 58(24): 5097-5109.

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References 48

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引物名称 Primer name	引物序列 Primer name Primer sequence (5′-3′)	用途 Purpose
seq-sgd13-F seq-sgd13-R	GATCGGCATTCTTCACTGTGG TGGAATGGCACTCCCTGAAC	鉴定sgd13突变位点的测序引物 Sequencing primers for identifying the sgd13 mutation site
gd13-MluCIF sgd13-MluCIR	TGCATGCTGCACCAGCTTTTCTAA AACGTATTGCCATTGCACGG	鉴定sgd13突变位点的dCAPS分子标记 dCAPS marker for genotyping the sgd13 mutation site
COM-sgd13-F COM-sgd13-R	GGACCTGACATGTTCAATCTCCT AATACCCGGGTTTGGTGCTT	互补载体构建 Complementary vector construction

组合 Combination	F₁植株表型 Phenotype of F₁plants	F₂植株数量 Number of F₂plants		χ² （3﹕1≈3.84）
组合 Combination	F₁植株表型 Phenotype of F₁plants	正常表型Normal phenotype	突变表型Mutant phenotype	χ² （3﹕1≈3.84）
南粳9108×sgd13 NJ9108×sgd13	正常表型Normal phenotype	98	22	2.844
sgd13×南粳9108 sgd13×NJ9108	正常表型Normal phenotype	143	57	1.307

染色体 Chromosome	物理位置 Physical location (bp)	基因型 Genotype	位置 Location	基因位点名称 Name of gene locus	功能类型 Function type
Chr.1	581447	G/A	基因间区 Intergenic	/	/
Chr.1	5569468	G/A	基因上游 Upstream	LOC_Os01g10504	/
Chr.1	7646648	G/A	基因间区 Intergenic	/	/
Chr.1	12711496	G/A	基因间区 Intergenic	/	/
Chr.1	24333007	G/A	基因间区 Intergenic	/	/
Chr.1	25001139	C/T	基因间区 Intergenic	/	/
Chr.1	25577375	C/T	基因间区 Intergenic	/	/
Chr.1	27410330	C/T	基因间区 Intergenic	/	/
Chr.1	30113852	C/T	基因间区 Intergenic	/	/
Chr.1	30191986	T/A	外显子 Exonic	LOC_Os01g52550	非同义突变 Non-synonymous mutation
Chr.1	32405502	C/T	基因间区 Intergenic	/	/
Chr.1	32928221	T/TA	基因下游 Downstream	LOC_Os01g56990	/
Chr.1	33733260	C/T	3′端非翻译区 3′-UTR	/	/
Chr.1	34069876	C/T	基因间区 Intergenic	/	/
Chr.1	34550111	T/A	基因上游 Upstream 基因下游 Downstream	/	/

Identification and Gene Mapping of Rice Grain Shape Mutant sgd13

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