籼稻品种基因组中逆转座子Tos17的鉴定与研究

doi:10.3864/j.issn.0578-1752.2025.15.001

中国农业科学 ›› 2025, Vol. 58 ›› Issue (15): 2933-2947.doi: 10.3864/j.issn.0578-1752.2025.15.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

籼稻品种基因组中逆转座子Tos17的鉴定与研究

罗嘉锐¹(), 吴三玲², 郭芾³, 刘振³, 宋婧含¹^,³, 谭瑗瑗¹^,⁴, 舒庆尧¹^,³^,^*()

¹ 浙江大学现代种业研究所/水稻生物育种全国重点实验室/浙江省作物种质创新与利用重点实验室，杭州 310058
² 浙江大学农生环测试中心，杭州 310058
³ 浙江大学海南研究院，海南三亚 572024
⁴ 浙江大学新农村发展研究院，杭州 310058

收稿日期:2025-02-08 接受日期:2025-04-01 出版日期:2025-07-30 发布日期:2025-07-30
通信作者:
舒庆尧，E-mail：qyshu@zju.edu.cn
联系方式: 罗嘉锐，E-mail：22216145@zju.edu.cn。
基金资助:
科技部“十四五”重点研发计划(2022YFD12007); 江苏省重点研发计划(BE2023336); 海南省自然科学基金高层次人才项目(322RC741); 浙江大学海南研究院专职科研人员启动项目(0201-6602-A12201)

Identification and Characterization of Retrotransposon Tos17 in the Genomes of Indica Rice

LUO JiaRui¹(), WU SanLing², GUO Fu³, LIU Zhen³, SONG JingHan¹^,³, TAN YuanYuan¹^,⁴, SHU QingYao¹^,³^,^*()

¹ The Advanced Seed Institute, Zhejiang University/State Key Laboratory of Rice Breeding & Biology/Zhejiang Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hangzhou 310058
² Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058
³ Hainan Institute of Zhejiang University, Sanya 572024, Hainan
⁴ The New Countryside Development Institute of Zhejiang University, Hangzhou 310058

Received:2025-02-08 Accepted:2025-04-01 Published:2025-07-30 Online:2025-07-30

摘要/Abstract

摘要：

【目的】 Tos17是水稻基因组中的一类逆转座子。在粳稻品种日本晴中，位于第7染色体上的一个Tos17（Tos17 ^Chr.7）在组织培养中可被激活。研究我国籼稻品种中Tos17的基因组学特征，确定其在组织培养中可否被激活而影响生物技术育种。【方法】从公共数据库中获取籼稻品种或杂交稻亲本的高质量基因组重测序数据，定制开发程序鉴定和分析Tos17的插入位点，并采用IGV软件和PCR验证鉴定结果。通过层次聚类和主成分分析对品种进行分类，基于全基因组单核苷酸多态性（single-nucleotide polymorphism，SNP）数据构建系统发育树，并运用Mantel检验评估其与Tos17单倍型的关联性。同时，采用农杆菌介导法培育籼稻品种成熟胚愈伤组织转化植株，并分析其Tos17数量的变化。【结果】开发了一个鉴定Tos17的程序Tos17-finder，在1 511份籼稻品种中共鉴定到23个插入不同位置的Tos17。12个Tos17位于已注释基因的内部或其上下游2 kb范围内，其余11个位于基因间区。1 511个品种在第10染色体上均有一个与日本晴一致的Tos17（Tos17 ^Chr.10），在第2染色体上有2个高频率出现的拷贝，即Tos17 ^Chr.2-1（79.0%）和Tos17 ^Chr.2-2（83.7%），但只有85个（5.6%）品种携带Tos17^Chr.7。Tos17在每个品种的平均拷贝数为4.0个，其中，有11个品种的Tos17拷贝数多达8个，还有35个品种只检测到Tos17 ^Chr.10。根据基因组SNP，将1 511个品种分为3个亚群，每个亚群均与Tos17单倍型存在一定相关性。采用农杆菌介导遗传转化，共培育5个籼稻品种的125株T₀转基因苗，并获得了高质量基因组重测序数据，经分析，未发现有新的Tos17插入。开发了一个能准确区分Tos17^Chr.7和其他Tos17的分子标记。【结论】籼稻品种中Tos17的基因组学特征与粳稻品种日本晴存在一定差异，可以用本试验开发的分子标记快速检测待测材料是否携带可被激活的Tos17^Chr.7。

关键词: Tos17, 籼稻, 全基因组重测序, 组织培养, 转座子基因组学, 转座活性

Abstract:

【Objective】 Tos17 is a type of retrotransposon in the rice genome. In the japonica variety Nipponbare, a Tos17 located on chromosome 7 (Tos17^Chr.7) can be activated during tissue culture. This study aims to reveal the genomic features of Tos17 of indica varieties in China and determine whether their Tos17 can be activated in tissue culture like in japonica rice, which may affect biotechnological breeding. 【Method】 High-quality genome resequencing data of indica varieties or hybrid parents were retrieved from public databases. An in-house program was developed to identify and analyze Tos17 insertion loci, confirmed by IGV visualization and PCR assays. The varieties were classified through hierarchical clustering and principal component analysis, a phylogenetic tree was constructed based on genome-wide single nucleotide polymorphism (SNP) data, and the association between varietal clusters and Tos17 haplotypes was assessed using Mantel test. Transgenic plants were generated by Agrobacterium -mediated transformation of mature embryo-derived callus of indica varieties, and the changes of Tos17 copy number were analyzed in 125 T₀transgenic plants.【Result】 23 distinct Tos17 insertion loci were identified in 1 511 indica varieties using the Tos17-finder, a program developed specifically for Tos17 identification. All varieties had a Tos17 on Chr.10 (Tos17^Chr.10) identical to the one in japonica rice Nipponbare, and there were two high-frequency Tos17 copies on Chr.2, i.e., Tos17^Chr.2-1 (79.0%) and Tos17^Chr.2-2 (83.7%), but only 85 (5.6%) varieties carried the Tos17^Chr.7 common to japonica rice. There were 4.0 Tos17 copies per variety on average, and while 11 varieties had up to 8 Tos17 copies, 35 only had a single Tos17, i.e., Tos17^Chr.10. Twelve Tos17 insertions were located within or 2 kb up- or down-stream of annotated genes, with the remaining 11 in intergenic regions. Phylogenetic analysis based on SNPs classified the 1 511 varieties into three subpopulations, each showing partial correlation with specific Tos17 haplotypes. No new Tos17 insertions were detected in the 125 T₀ transgenic seedlings of 5 indica varieties. A molecular marker capable of accurately distinguishing Tos17^Chr.7 from other Tos17s was developed. 【Conclusion】 The genomic features of Tos17 in indica rice varieties differ from those in japonica rice variety Nipponbare. The developed molecular marker can be used to determine readily whether the test materials carry the activatable Tos17^Chr.7.

Key words: Tos17, indica rice, whole-genome resequencing, tissue culture, transposon genomics, transposition activity

罗嘉锐, 吴三玲, 郭芾, 刘振, 宋婧含, 谭瑗瑗, 舒庆尧. 籼稻品种基因组中逆转座子Tos17的鉴定与研究[J]. 中国农业科学, 2025, 58(15): 2933-2947.

LUO JiaRui, WU SanLing, GUO Fu, LIU Zhen, SONG JingHan, TAN YuanYuan, SHU QingYao. Identification and Characterization of Retrotransposon Tos17 in the Genomes of Indica Rice[J]. Scientia Agricultura Sinica, 2025, 58(15): 2933-2947.

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数据来源Data source	品种类型Type of rice variety	品种数量No. of varieties	参考文献Reference
PRJNA656900*	两系法核基因雄性不育系Two-line genic male sterile line	82	[16]
	两系法恢复系Two-line restorer	70
	三系法恢复系Three-line restorer	249
	三系法雄性不育保持系Three-line male sterility maintainer	15
	常规品种Conventional variety	271
	细胞质雄性不育Cytoplasmic male sterile rice	200
	种质资源Germplasm accession	131
PRJNA880974**	籼稻引进品种XIC (Xian Introduced Cultivars)	4	[17]
	籼稻地方品种XL (Xian Landraces)	34
	籼稻主栽品种XMC (Xian Major Cultivars)	169
CRA000167***	种质资源Germplasm	286	[18]

材料 Material	Q20 (%)	Q30 (%)	定位读序数 Mapped reads (bp)	定位率 Mapped rate (%)	基因组覆盖率 Genome coverage (%)	测序深度 Sequencing depth (×)
DR950	96.2(95.2-98.2)	89.6(86.9-95.1)	78663682 (74182194-80276648)	96.4(96.3-96.6)	87.2(86.8-87.5)	27.4(25.9-28.0)
GM03	98.6(98.1-99.0)	89.6(86.9-95.1)	78381573(56149050-80293264)	95.6(95.4-96.3)	86.6(86.4-86.8)	27.3(19.6-28.0)
R17	95.8(95.5-96.1)	88.2(87.5-89.0)	79684843(77671050-80297370)	96.1(96.1-96.1)	87.2(87.2-87.1)	27.8(27.1-28.0)
翠玉B Cuiyu B	96.2(95.7-96.9)	89.4(88.1-91.4)	74326250(46121258-80299402)	96.4(96.3-96.4)	86.9(86.2-87.4)	25.9(16.1-28.0)
R7954	97.6(96.1-98.7)	92.6(89.7-95.0)	78062693(27615630-80309870)	96.1(95.5-97.1)	88.0(87.1-88.7)	27.2(9.6-28.0)

籼稻品种基因组中逆转座子Tos17的鉴定与研究

Identification and Characterization of Retrotransposon Tos17 in the Genomes of Indica Rice

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