Development and Prospects of Rice Pan-genomics: Important Tools and Applications

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

Abstract

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

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.

Figures/Tables 4

References 47

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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]

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]