水稻泛基因组学的发展与前景：重要工具与应用

doi:10.13560/j.cnki.biotech.bull.1985.2024-0669

摘要/Abstract

摘要：

与单个基因组不同，泛基因组一般是指包含一个物种或群体中全部基因组信息的数据集。近十年来，泛基因组学在水稻中已逐步成为研究热点，相关泛基因组成果和工具已在群体遗传学、进化生物学和生物育种实践等多个下游研究领域中获得广泛应用。本文聚焦于水稻泛基因组学的发展历程与应用前景，回顾了水稻泛基因组学的内涵发展和研究成果的时间线，总结了现有的水稻泛基因组代表性重要成果工具及其在多个领域中的主要应用，展望了其面临的挑战和发展前景。

关键词: 水稻泛基因组, 图形泛基因组, 数据库, 结构变异, 生物育种

Abstract:

Unlike a single genome, a pan-genome generally refers to a data set that contains all genomic information in a species or population. Over the past decade, pan-genomics has gradually become a research hotspot in rice, and relevant pan-genomes and tools have been widely applied in many downstream research fields such as population genetics, evolutionary biology and biological breeding practices. This paper focuses on the development process and application prospect of rice pan-genomics, reviews the development of connotation of rice pan-genomics and the timeline of its research results, summarizes the existing representative and important achievement tools of rice pan-genomics and their main applications in different fields, and looks forward to the challenges and development prospects for rice pan-genomics.

Key words: rice pan-genome, graph-based pan-genome, database, structural variation, biological breeding

贺文闯, 许强, 钱前, 商连光. 水稻泛基因组学的发展与前景：重要工具与应用[J]. 生物技术通报, 2024, 40(10): 9-18.

HE Wen-chuang, XU Qiang, QIAN Qian, SHANG Lian-guang. Development and Prospects of Rice Pan-genomics: Important Tools and Applications[J]. Biotechnology Bulletin, 2024, 40(10): 9-18.

图/表 4

图1 水稻泛基因组学的发展历程 A：泛基因组定义的概念图示；B：泛基因组构建方法和组成形式的发展；C：水稻泛基因组学研究的发展时间线；时间线上的每个分支代表一个泛基因组数据集，两个数字展示了其对应的群体大小（下）和被非综述性论文引用的次数（上）；*代表该泛基因组研究产出了可公开访问的数据库平台或友好分析工具；被引次数来源于Web of Science数据库，统计截至2024年6月17日

Fig. 1 Development of rice pan-genomics A: Illustration of the pan-genome definition. B: Development of pan-genome construction methods and constituent forms. C: Development timeline of rice pan-genomics studies. Each branch of the timeline iindicates a pan-genomic dataset, with two numbers showing its corresponding population size（bottom）and the number of citations to non-review papers（top）. * indicates the production of a publicly accessible database or friendly analytical tool for the pan-genomic study. Number of citations are from the Web of Science database as of June 17, 2024

表1 已发表的水稻泛基因组研究汇总

Table 1 Summary of published pan-genome studies in rice

构建方法 Construction method	发表时间 Published date	群体大小 Population size	群体组成 Species	测序数据Sequencing data	单基因组资源Genome resource	泛基因组资源Pan-genome resource	泛基因资源Pan-gene resource	变异资源 Variant resource	数据库 Database	潜在应用 Potential application				参考文献 Reference
构建方法 Construction method	发表时间 Published date	群体大小 Population size	群体组成 Species	测序数据Sequencing data	单基因组资源Genome resource	泛基因组资源Pan-genome resource	泛基因资源Pan-gene resource	变异资源 Variant resource	数据库 Database	单基因组参考 A single genomic reference	泛基因组参考Pan-genomic reference	GWAS等研究GWAS etc.	单倍型分析 Haplotype analysis	参考文献 Reference
Map-to-pan	2018	3 010	Os	Illumina	×	√	√	SNP/InDel/ SV	√	×	√	√	√	[10]
	2021	239	Osj	Illumina	×	√	√	SNPs/PAV	×	×	√	√	√	[11]
	2023	60	Os	Illumina	×	√	√	SNP/PAV	×	×	√	×	√	[12]
	2024	249	Ogla/Ob	Illumina	×	√	√	无	×	×	√	×	×	[13]
	2024	30	Oa/ Ogra/Ol	Illumina	×	√	√	SNP/PAV	×	×	√	×	√	[14]
全基因组比对Whole genome alignment	2014	3	Os	Illumina	√	×	冗余	无	×	√	×	×	√	[8]
	2017	3	Ogla	Illumina	√	×	冗余	无	×	√	×	×	√	[9]
	2018	66	Os/Or	Illumina	√	×	√	SNP/InDel	√	√	×	×	√	[15]
	2020	16	Os	Illumina/Pacbio/Bionano	√	×	×	InDel/SV	×	√	×	×	√	[16]
	2021	4	Os	Illumina/Pacbio	√	×	√	SNP/InDel/SV	×	√	×	×	√	[17]
	2022	111	Or/Os	Illumina/Nanopore	√	√	√	SV	×	√	√	×	√	[6]
	2022	108	Os	Illumina	√	√	√	InDel/PAV	×	√	√	×	√	[18]
	2023	74	Or/Os/杂草稻	PacBio（12）/Hi-C（4）	√	×	√	SNP/PAV	×	√	×	×	√	[19]
	2023	16	Os	Iso-Seq/RNA-Seq	[16]*	×	√	可变剪切事件	√	√	×	×	√	[20]
	2023	12	Os/Ogla	[21]*	[21]*	√	√	PAV	×	√	√	×	√	[7]
图形泛基因组Graph-based pan-genome	2021	33	Os/Ogla	Illumina/Pacbio/Bionano（3）	√	√	√	SV/gCNV	√	√	√	×	√	[21]
图形泛基因组Graph-based pan-genome	2022	251	Os/Or/ Ogla/Ob	Illumina/Nanopore/Hi-C（4）	√	√	√	SV	√	√	√	√	√	[22]

表1 已发表的水稻泛基因组研究汇总

Table 1 Summary of published pan-genome studies in rice

构建方法 Construction method	发表时间 Published date	群体大小 Population size	群体组成 Species	测序数据Sequencing data	单基因组资源Genome resource	泛基因组资源Pan-genome resource	泛基因资源Pan-gene resource	变异资源 Variant resource	数据库 Database	潜在应用 Potential application				参考文献 Reference
构建方法 Construction method	发表时间 Published date	群体大小 Population size	群体组成 Species	测序数据Sequencing data	单基因组资源Genome resource	泛基因组资源Pan-genome resource	泛基因资源Pan-gene resource	变异资源 Variant resource	数据库 Database	单基因组参考 A single genomic reference	泛基因组参考Pan-genomic reference	GWAS等研究GWAS etc.	单倍型分析 Haplotype analysis	参考文献 Reference
Map-to-pan	2018	3 010	Os	Illumina	×	√	√	SNP/InDel/ SV	√	×	√	√	√	[10]
	2021	239	Osj	Illumina	×	√	√	SNPs/PAV	×	×	√	√	√	[11]
	2023	60	Os	Illumina	×	√	√	SNP/PAV	×	×	√	×	√	[12]
	2024	249	Ogla/Ob	Illumina	×	√	√	无	×	×	√	×	×	[13]
	2024	30	Oa/ Ogra/Ol	Illumina	×	√	√	SNP/PAV	×	×	√	×	√	[14]
全基因组比对Whole genome alignment	2014	3	Os	Illumina	√	×	冗余	无	×	√	×	×	√	[8]
	2017	3	Ogla	Illumina	√	×	冗余	无	×	√	×	×	√	[9]
	2018	66	Os/Or	Illumina	√	×	√	SNP/InDel	√	√	×	×	√	[15]
	2020	16	Os	Illumina/Pacbio/Bionano	√	×	×	InDel/SV	×	√	×	×	√	[16]
	2021	4	Os	Illumina/Pacbio	√	×	√	SNP/InDel/SV	×	√	×	×	√	[17]
	2022	111	Or/Os	Illumina/Nanopore	√	√	√	SV	×	√	√	×	√	[6]
	2022	108	Os	Illumina	√	√	√	InDel/PAV	×	√	√	×	√	[18]
	2023	74	Or/Os/杂草稻	PacBio（12）/Hi-C（4）	√	×	√	SNP/PAV	×	√	×	×	√	[19]
	2023	16	Os	Iso-Seq/RNA-Seq	[16]*	×	√	可变剪切事件	√	√	×	×	√	[20]
	2023	12	Os/Ogla	[21]*	[21]*	√	√	PAV	×	√	√	×	√	[7]
图形泛基因组Graph-based pan-genome	2021	33	Os/Ogla	Illumina/Pacbio/Bionano（3）	√	√	√	SV/gCNV	√	√	√	×	√	[21]
图形泛基因组Graph-based pan-genome	2022	251	Os/Or/ Ogla/Ob	Illumina/Nanopore/Hi-C（4）	√	√	√	SV	√	√	√	√	√	[22]

图2 水稻泛基因组研究的非综述文献引用的主要领域分布情况 * WOS数据库中MeSH Headings关键词的统计结果（参与统计的文献总数n=859，单个词条的引用量≥50）。此处仅展示水稻重要领域相关词条结果，描述相似或者领域相近的关键词仅展示其一

Fig. 2 Distribution of major fields of non-review citations for rice pan-genome studies * statistical results of MeSH Headings Keywords in the WOS database（the total number of literatures participating in the statistics n=859, the number of citations for a single entry ≥50）. Only the results of terms related to important fields of rice are shown here, and only one keyword describing similar or similar fields is shown

图3 水稻泛基因组学工具的主要应用进化和驯化图中元素根据Chen等[25]进行了修改；生物育种和智慧育种图中元素根据Ferrero-Serrano等[26]进行了修改

Fig. 3 Main applications of rice pan-genomics tools The elements in the evolution and domestication diagram are modified according to Chen et al[25]. The elements in the diagram for biological breeding and intelligent breeding are modified according to Ferrero-Serrano et al[26]

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