一个浙粳99短穗小粒突变体的鉴定及转录组分析

doi:10.16819/j.1001-7216.2024.231111

中国水稻科学 ›› 2025, Vol. 39 ›› Issue (1): 67-81.DOI: 10.16819/j.1001-7216.2024.231111

一个浙粳99短穗小粒突变体的鉴定及转录组分析

梁楚炎¹^,², 曾维², 王洁冰¹^,³, 叶靖², 巫明明², 翟荣荣², 张小明², 张恒木³^,^*(), 叶胜海²^,^*()

¹中国计量大学生命科学学院，杭州 310018
²浙江省农业科学院作物与核技术利用研究所，杭州 310021
³浙江省农业科学院病毒学与生物技术研究所，杭州 310021

收稿日期:2023-11-14 修回日期:2024-03-04 出版日期:2025-01-10 发布日期:2025-01-14
通讯作者: *email: zhhengmu@tsinghua.org.cn;
shenghaiye@163.com
基金资助:
浙江省水稻新品种选育重大科技专项(2021C02063-5);海南省重点研发计划资助项目(ZDYF2023XDNY086);浙江省省部共建农产品质量安全危害因子与风险防控国家重点实验室课题(2010DS700124);浙江省“尖兵”“领雁”研发攻关计划资助项目(2023C02055);浙江省“尖兵”“领雁”研发攻关计划资助项目(2022C02034)

Characterization and Transcriptome Analysis of a Mutant with Short Panicle and Small Grain from Zhejing 99

LIANG Chuyan¹^,², ZENG Wei², WANG Jiebing¹^,³, YE Jing², WU Mingming², ZHAI Rongrong², ZHANG Xiaoming², ZHANG Hengmu³^,^*(), YE Shenghai²^,^*()

¹College of Life Science, China Jiliang University, Hangzhou 310018, China
²Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
³Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2023-11-14 Revised:2024-03-04 Online:2025-01-10 Published:2025-01-14
Contact: *email: zhhengmu@tsinghua.org.cn;
shenghaiye@163.com

摘要/Abstract

摘要：

【目的】探明浙粳99优良穂型的形成机制，为水稻穗型发育机制研究及其育种应用提供科学依据。【方法】利用EMS诱变浙粳99获得短穗小粒突变体，借助分子标记获得连锁区间，采用RNA-Seq及DNA测序确定候选基因，并利用激光共聚焦显微镜观察突变基因的亚细胞定位。使用转录组测序的方法对该突变体的基因表达情况进行分析。【结果】Ossp3与浙粳99在株型、穗型以及粒型上均存在差异。该突变表型由候选基因Os02g0450000发生碱基插入引起。亚细胞定位结果显示该基因产物定位于细胞核。Ossp3幼穗出现329个差异表达基因（DEG），主要分布在1、3和4号染色体上，KEGG富集分析显示，这些差异表达基因主要集中在植物激素信号转导途径、MARK信号通路-植物等生物学过程。相关基因表达分析显示进化上保守的植物特异性基因OsSP3通过MAPK信号通路或与bZIP转录因子作用影响生长素、细胞分裂素含量及其对应信号途径，实现对稻穗发育的调控。【结论】优良穗型品种浙粳99 Os02g0450000基因突变会产生短穗小粒的表型，其生物学功能通过核定位实现，RNA-Seq分析表明该突变基因可能通过影响生长素与细胞分裂素信号通路协同调控稻穗的生长发育，同时很可能通过与OsbZIP47直接或间接作用调控粒型。

关键词: 短穗小粒, 表型鉴定, RNA-Seq, 转录组分析

Abstract:

【Objective】This study aims to explore the formation mechanism of the superior panicle type in Zhejing 99 and lays a scientific foundation for understanding the developmental mechanisms of rice panicle types and their breeding applications.【Method】We used ethyl methanesulfonate (EMS) to induce mutations in Zhejing 99, resulting in a short panicle and small grain mutant. Molecular markers were employed to obtain linkage intervals, and candidate genes were identified through RNA sequencing (RNA-Seq) and DNA sequencing. The subcellular localization of the mutant gene was observed using a laser confocal microscopy. Additionally, transcriptome sequencing was conducted to analyze gene expression and the expression characteristics of related genes.【Result】Phenotypic identification revealed differences in plant type, panicle type, and grain type of the Ossp3 mutant compared to Zhejing 99. The mutant phenotype was caused by a base insertion in the candidate gene Os02g0450000. Subcellular localization showed that the gene product is located in the nucleus. In the young panicles of the Ossp3 mutant, 329 differentially expressed genes (DEGs) were identified, primarily distributed on chromosomes 1, 3, and 4. KEGG enrichment analysis highlighted significant biological processes, including plant hormone signaling pathways and MAPK signaling pathways in plants. Analysis of related gene expression suggests that the evolutionarily conserved plant-specific gene OsSP3 influences auxin and cytokinin content and their corresponding signaling pathways through the MAPK signaling pathway or by interacting with bZIP transcription factors, thereby regulating rice panicle development.【Conclusion】The gene mutation in the superior panicle type variety Zhejing 99, specifically in Os02g0450000, results in the phenotype of short panicles and small grains. Its biological function is mediated through nuclear localization. RNA-Seq analysis indicates that the mutated gene may synergistically regulate the growth and development of rice panicles by affecting auxin and cytokinin signaling pathways and may also directly or indirectly influence grain type through interaction with OsbZIP47.

Key words: short panicle and small grain, phenotypic identification, RNA-Seq, transcriptome analysis

梁楚炎, 曾维, 王洁冰, 叶靖, 巫明明, 翟荣荣, 张小明, 张恒木, 叶胜海. 一个浙粳99短穗小粒突变体的鉴定及转录组分析[J]. 中国水稻科学, 2025, 39(1): 67-81.

LIANG Chuyan, ZENG Wei, WANG Jiebing, YE Jing, WU Mingming, ZHAI Rongrong, ZHANG Xiaoming, ZHANG Hengmu, YE Shenghai. Characterization and Transcriptome Analysis of a Mutant with Short Panicle and Small Grain from Zhejing 99[J]. Chinese Journal OF Rice Science, 2025, 39(1): 67-81.

图/表 15

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引物名称 Name	引物序列 Sequence (5’-3’)
OsSP3-F1	ATGTCGACGGCCGCCAAGGAGGA
OsSP3-R1	TTACACTGAGGAGCGCTCCAAAC
OsSP3-F2	AACACGGGGGACTTTGCAACATGTCGACGGCCGCCAAGG
OsSP3-R2	GACAGAGCTAGTTACATTACACTGAGGAGCGCTCCAAACT
OsSP3-F3	GGGGCCTGGGGTACCCATGTCGACGGCCGCCAAGG
OsSP3-R3	CGCCCTTGCTCACGTCGACCACTGAGGAGCGCTCCAAACT

引物名称 Name	引物序列 Sequence (5’-3’)
OsSP3-F1	ATGTCGACGGCCGCCAAGGAGGA
OsSP3-R1	TTACACTGAGGAGCGCTCCAAAC
OsSP3-F2	AACACGGGGGACTTTGCAACATGTCGACGGCCGCCAAGG
OsSP3-R2	GACAGAGCTAGTTACATTACACTGAGGAGCGCTCCAAACT
OsSP3-F3	GGGGCCTGGGGTACCCATGTCGACGGCCGCCAAGG
OsSP3-R3	CGCCCTTGCTCACGTCGACCACTGAGGAGCGCTCCAAACT

组合 Combination	F₁正常表型植株 Number of normal plants in F₁	F₂					χ²_（3:1）
组合 Combination	F₁正常表型植株 Number of normal plants in F₁	总株数 Total plant number	正常表型植株 Normal plants		突变表型植株 Mutant plants		χ²_（3:1）
Ossp3/WT	5	355		265		90	0.0117

组合 Combination	F₁正常表型植株 Number of normal plants in F₁	F₂					χ²_（3:1）
组合 Combination	F₁正常表型植株 Number of normal plants in F₁	总株数 Total plant number	正常表型植株 Normal plants		突变表型植株 Mutant plants		χ²_（3:1）
Ossp3/WT	5	355		265		90	0.0117

变异位点 Mutation site	SNP/InDel	参考基因组碱基 Reference genome bases	样品wt碱基 Sample wt base	样品sp3碱基 Sample sp3 base	候选基因 Candidate gene	原因 Reason
17287987	SNP	A	A	G	否No	同义突变GGT/GGC→Gly
17489881	SNP	C	C	T	否No	其他参考基因组碱基为T
18059754	SNP	A	A	G	否No	其他参考基因组碱基为G
18121601	SNP	C	C	A	否No	其他参考基因组碱基为A
19270791	SNP	T	T	G	否No	其他参考基因组碱基为G
19309819	SNP	A	A	G	否No	其他参考基因组碱基为G
20348604	SNP	G	G	A	否No	其他参考基因组碱基为A
14683027	InDel	A	A	AAC	是Yes	移码突变

一个浙粳99短穗小粒突变体的鉴定及转录组分析

Characterization and Transcriptome Analysis of a Mutant with Short Panicle and Small Grain from Zhejing 99

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GO: ID	GO条目 GO term	基因数Number	GO ID	GO条目 GO term	基因数 Number
GO:0008150	Biological process	179	GO:0043231	Intracellular membrane-bounded organelle	94
GO:0009987	Cellular process	144	GO:0043227	Membrane-bounded organelle	94
GO:0008152	Metabolic process	141	GO:0016020	Membrane	81
GO:0071704	Organic substance metabolic process	127	GO:0031224	Intrinsic component of membrane	70
GO:0044238	Primary metabolic process	118	GO:0016021	Integral component of membrane	63
GO:0044237	Cellular metabolic process	117	GO:0003674	Molecular function	189
GO:0006807	Nitrogen compound metabolic process	90	GO:0005488	Binding	119
GO:0043170	Macromolecule metabolic process	86	GO:0003824	Catalytic activity	104
GO:0044260	Cellular macromolecule metabolic process	75	GO:1901363	Heterocyclic compound binding	81
GO:0065007	Biological regulation	61	GO:0097159	Organic cyclic compound binding	81
GO:0005575	Cellular component	183	GO:0043167	Ion binding	55
GO:0110165	Cellular anatomical entity	182	GO:0016787	Hydrolase activity	45
GO:0005622	Intracellular anatomical structure	110	GO:0003676	Nucleic acid binding	42
GO:0043229	Intracellular organelle	97	GO:0003677	DNA binding	37
GO:0043226	Organelle	97	GO:0016740	Transferase activity	35

ID	KEGG条目 KEGG term	基因数Number	ID	KEGG条目 KEGG term	基因数Number
ko01100	Metabolic pathways	57	ko00904	Diterpenoid biosynthesis	3
ko01110	Biosynthesis of secondary metabolites	28	ko00250	Alanine, aspartate and glutamate metabolism	3
ko04075	Plant hormone signal transduction	11	ko00051	Fructose and mannose metabolism	3
ko00196	Photosynthesis - antenna proteins	8	ko00195	Photosynthesis	3
ko00940	Phenylpropanoid biosynthesis	7	ko00430	Taurine and hypotaurine metabolism	2
ko01200	Carbon metabolism	7	ko00650	Butanoate metabolism	2
ko00520	Amino sugar and nucleotide sugar metabolism	6	ko00410	beta-Alanine metabolism	2
ko00500	Starch and sucrose metabolism	6	ko00240	Pyrimidine metabolism	2
ko00710	Carbon fixation in photosynthetic organisms	5	ko00999	Biosynthesis of plant secondary metabolites	2
ko04016	MAPK signaling pathway - plant	5	ko00260	Glycine, serine and threonine metabolism	2
ko04626	Plant-pathogen interaction	5	ko00531	Glycosaminoglycan degradation	1
ko00630	Glyoxylate and dicarboxylate metabolism	4	ko00740	Riboflavin metabolism	1
ko00480	Glutathione metabolism	4

ID	基因符号 Symbol	注释 Innovation	表型 Phenotype	log₂(Fold Change)
Os03g0180800	OsJAZ9; OsTIFY11a	TIFY家族基因（茉莉酸信号通路基因）	过表达导致脱落酸(ABA)和茉莉酸(JA)水平升高，降低了叶片宽度和气孔密度。RNAi导致缺水胁迫更敏感，植株茎部的生长只有野生型的60%^[25]-[28]	−3.79
Os09g0111100	OsCYCD3	D型细胞周期蛋白	敲除突变体分支数量减少，腋生分生组织和茎尖分生组织（SAM）活性受到损害^[29]	1.16
Os06g0696600		糖基水解酶家族	未知	−3.26
Os11g0141900	OsNH5.1; OsBOP2	NPR1类似基因; BOP基因	过表达促进叶鞘发育、抑制叶片发育。基因冗余控制小穗器官发育，护颖更长^[30]-[31]	1.58
Os01g0382400		SCP样细胞外蛋白	未知	4.00
Os02g0200900		F-box蛋白; E3泛素连接酶	OsEBF2与OsEIL1互作，过表达增强褐飞虱抗性，抗性机制通过抑制乙烯应答因子基因的表达来降低乙烯含量^[32]	−1.30
Os03g0322700	OsbZIP29	bZIP转录因子	bZIP转录因子从开花到穗和种子发育不同阶段，存在特异和共表达模式^[33]	2.41
Os06g0265400	OsbZIP47	bZIP转录因子	突变体粒宽和粒重增加，过表达籽粒变窄^[34]	1.40
Os04g0691100	OsSAPK5	应激活化蛋白激酶	OsSAPK5能被高渗透胁迫激活^[35]	−1.05
Os10g0191300		SCP样细胞外蛋白	未知	4.78
Os11g0221000	OsIAA27	OsAux/IAAs家族基因（生长素信号通路基因）	未知	−1.41

ID	基因符号 Gene symbol	log₂(Fold Change)	ID	基因符号 Gene symbol	log₂(Fold Change)
Os01g0813100	OsbZIP09	0.17	Os04g0559800	OsMKKK10	0.10
Os06g0601500	OsbZIP48	−0.18	Os02g0787300	OsMKK4	0.13
Os07g0686100	OsbZIP62	0.82	Os05g0115800	OsMKP1	0.08
Os06g0162800	OsMADS5	0.30	Os06g0154500	OsMAPK6	−0.01
Os03g0753100	OsMADS34	0.05	Os01g0699500	OsMKKK70	−1.88
Os04g0411400	RCN4	2.61	Os03g0786400	DST	−0.358
Os12g0601300	OsIAA30	−0.70	Os06g0203800	OsER1	0.45
Os03g0187500	OsAFB6	0.36	Os06g0157700	Hd3a	2.53
Os01g0625900	OsOFP2	0.46	Os06g0157500	RFT1	FPKM=0
Os04g0442300	OsRR1	0.87	Os09g0540800	OsbZIP77	2.48
Os10g0463400	Ehd1	FPKM=0	Os08g0430500	Gf14	−0.27
Os01g0197700	Gn1a	0.32	Os05g0489700	OsbZIP42	0.16

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