作物泛基因组研究进展与展望

doi:10.3864/j.issn.0578-1752.2025.11.001

Abstract

Abstract:

The global population continues to rise and climate change imposes severe challenges on food supply, the issue of food security has become increasingly prominent. To meet the growing demand for food, enhancing crop yield and improving environmental adaptability have become critical goals in agriculture. Under this situation, genomics is regarded as an essential method for accelerating crop breeding, as it enables the in-depth exploration and utilization of superior functional genes to not only boost crop productivity but also strengthen stress tolerance and adaptability, thereby providing robust support for ensuring global food security and achieving sustainable agricultural development. Nonetheless, the traditional single-reference genome often fails to capture the entire spectrum of genomic variations accumulated during crop domestication and improvement, which constrains our understanding of functional genes and their regulatory networks. With the continual advancement of high-throughput sequencing technologies, genomics research has now entered the pangenomics era. By integrating multiple high-quality genomes into a comprehensive catalog of genomic content, researchers can precisely identify a variety of genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations (SVs), thereby capturing the extensive genetic diversity present across different cultivars, subspecies, and wild relatives. Pangenomics framework greatly facilitates the exploration of superior functional genes. Moreover, by combining pangenomic data with other multi-omics datasets (e.g., transcriptomics, proteomics, and epigenomics), researchers can accurately identify superior functional genes, enabling the provision of more targeted and accurate genetic loci for molecular breeding. With emerging gene-editing tools such as CRISPR-Cas9, researchers can further modify essential genetic loci in a directed manner to remove undesirable traits or reinforce resistance to environmental stressors. This will lay a foundation for cultivating the next generation of crops that exhibit higher yield, improved quality, and enhanced resilience. This review summarizes recent developments in major pangenome construction methods and formats, and systematically reviews the progress made in crop pangenomes as well as their applications in crop breeding improvement. It also discusses the challenges pangenomics faces in future crop breeding, offering insights into leveraging pangenome resources for crop genetic improvement, and ultimately provides new perspectives and strategies for future molecular breeding.

Key words: molecular breeding, pangenome, structural variations, new productivity, genetic diversity

WANG Hui, DING BaoPeng, LI YuXian, REN QuanRu, ZHOU Hai, ZHAO JunLiang, HU HaiFei. Research Progress and Prospects on Crop Pan-Genomics[J].Scientia Agricultura Sinica, 2025, 58(11): 2045-2061.

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Figures/Tables 4

Table 1

The development and application of genomic sequencing technologies"

技术类型 Technology type	技术名称 Technology name	时间 Time	优势与劣势 Advantage and disadvantage	应用实例 Application example
第一代测序及组装 First generation sequencing and assembly	Sanger测序 Sanger sequencing	1977 ^[11]	优势：具备高准确性，低错误率，测序结果易于分析和解释。劣势：测序通量低导致测序效率低，难以满足大规模基因组测序的需求。 Advantages: It possesses high accuracy with a low error rate, making the sequencing results easy to analyze and interpret. Disadvantages: The low sequencing throughput results in inefficient sequencing, making it difficult to meet the demands of large-scale genomic sequencing.	水稻基因组^[4]、高粱基因组^[13]、玉米基因组^[14] Rice genome, Sorghum genome, Maize genome
第一代测序及组装 First generation sequencing and assembly	BACs克隆测序 BACs cloning and sequencing	1992 ^[38]	优势：高分辨率，低嵌合率，高遗传稳定性，可容纳300 kb DNA片段，有助于获得高质量的基因组序列。劣势：文库的构建和筛选过程相对复杂，BAC克隆的测序和组装成本较高。 Advantages: High resolution, low chimeric rate, good genetic stability, and the ability to accommodate up to 300 kb DNA fragments, contributing to the generation of high-quality genomic sequences. Disadvantages: The processes of library construction and screening are relatively complex, and the sequencing and assembly costs of BAC clones are high.
第二代测序及组装 Next-generation sequencing and assembly	Illumina短读长NGS Illumina Short Read NGS	2008 ^[39]	优势：低成本、高通量，高准确性。劣势：读长较短，在复杂基因组及重复序列的组装时面临较大困难。 Advantages: Low cost, high throughput, and high accuracy. Disadvantages: Shorter read lengths pose challenges for the assembly of complex genomes and repetitive sequences.	芥菜基因组^[16]、生菜基因组^[17]、油菜基因组^[18]、大豆基因组^[19] Mustard genome, Lettuce genome, Rapeseed genome, Soybean genome
第三代测序及组装 Third generation sequencing and assembly	PacBio测序 PacBio sequencing	2023 ^[40]	优势：PacBio HiFi读长高达15—20 kb，具有高分辨率和精准性，从而提高基因组组装的连续性和完整性。劣势：测序成本较高，在大规模项目中的应用可能受到限制。 Advantages: PacBio HiFi offers read lengths of up to 15-20 kb, high resolution, and accuracy, thereby enhancing the continuity and completeness of genome assembly. Disadvantages: The sequencing cost is relatively high, which may limit its application in large-scale sequencing projects.	面包小麦基因组^[27]、马铃薯基因组^[28] Bread wheat genome, Potato genome
第三代测序及组装 Third generation sequencing and assembly	Nanopore测序 Nanopore sequencing	2021 ^[29]	优势：Ultra-long超长读长，最长读长可达1 Mb。适用于从头组装基因组和解析复杂的结构变异。劣势：测序错误率相对较高，测序成本高。 Advantages: Ultra-long read lengths, with the longest reads reaching up to 1 Mb, making it suitable for de novo genome assembly and resolving complex structural variations. Disadvantages: Relatively high sequencing error rates and high sequencing costs.	水稻基因组^[33]、珍珠粟基因组^[34] Rice genome, Pearl millet genome
混合组装策略 Hybrid assembly strategy	二代测序+三代测序混合组装 Hybrid assembly using second-generation and third-generation sequencing	2012 ^[41]	优势：三代测序的长读长优势可以弥补二代测序在重复序列组装上的不足，生成更完整、更连续的基因组序列。二代测序可用于校正三代测序，从而提高测序准确性。劣势：二代和三代测序数据在读长、错误模式和覆盖度等方面存在差异，整合这些数据进行组装需要复杂的算法和计算资源。 Advantages: The long read lengths of third-generation sequencing can compensate for the shortcomings of second-generation sequencing in assembling repetitive sequences, generating more complete and contiguous genome sequences. Second-generation sequencing can be used to correct third-generation sequencing, thereby improving its accuracy. Disadvantages: There are differences between second- and third- generation sequencing data in terms of read length, error patterns, and coverage. Integrating these data for assembly requires complex algorithms and computational resources.	拟南芥基因组^[42]、马铃薯基因组^[43] Arabidopsis genome, Potato genome
混合组装策略 Hybrid assembly strategy	PacBio HiFi测序技术+Nanopore超长读长测序技术+HiC染色质构象捕获技术 PacBio HiFi+Nanopore Ultra-long+HiC	2022 ^[35]	优势：综合了长读长、高准确性和三维基因组结构信息，可实现无间隙基因组组装。劣势：成本较高，分析技术复杂性较高，需要较多的计算资源及相应的生物信息分析工具。 Advantages: Combining long read lengths, high accuracy, and three- dimensional genome structure information enables gapless genome assembly. Disadvantages: It is costly, involves complex analytical algorithm, and requires substantial computational resources as well as specialized bioinformatics analysis tools.	玉米T2T（端粒到端粒）基因组^[36]和高粱T2T基因组^[37] Maize T2T (telomere-to- telomere) genome, Sorghum T2T genome

Table 1

Table 2

Overview of current pan-genomic studies in plants and crops"

泛基因组构建方法 Method for pangenome construction	物种名 Species names	品种个数 Number of varieties	测序方法 Sequencing methods	参考文献 References
	棉花Gossypium hirsutum	344	Illumina HiSeq PacBio	[56]
从头组装、比较基因组De novo assembly, Comparative genomics	西瓜Citrullus lanatus	547	Illumina PacBio	[48]
	西瓜Citrullus lanatus	27	Illumina HiSeq PacBio HiFi	[49]
	西瓜Citrullus lanatus	400	Illumina	[50]
	大麦Hordeum vulgare	20	Illumina HiSeq PacBio	[55]
	大麦Hordeum vulgare	76	Illumina NovaSeq PacBio HiFi	[78]
	瓠Lagenaria siceraria	197	Illumina NextSeq	[57]
	珍珠粟Pennisetum glaucum	10	Illumina Pacbio HiFi	[61]
	地钱Marchantia polymorpha	133	Illumina HiSeq PacBio HiFi	[65]
	亚洲栽培稻和普通野生稻 Oryza sativa and Oryza rufipogon	111	PacBio	[47]
	杨树Populus przewalskii Maxim	19	Illumina HiSeq Nanopore	[63]
	梨Pyrus spp.	7	Illumina HiSeq PacBio HiFi	[58]
	土豆Solanum tuberosum	296	Illumina HiSeq	[51]
	土豆Solanum tuberosum	42	PacBio HiFi	[28]
	玉米Zea mays	14	Illumina HiSeq PacBio	[79]
	玉米Zea mays	26	PacBio	[53]
	甘蓝型油菜Brassica napus	8	Illumina HiSeq PacBio	[54]
从头组装、图形化泛基因组 De novo assembly, Graph-based pangenome	甘蓝Brassica oleracea	11	PacBio HiFi	[67]
	栽培和野生大豆 Glycine max and Glycine soja	26	Illumina HiSeq PacBio	[80]
	谷子Setaria italica	110	Illumina NovaSeq Pacbio	[81]
	番茄Solanum lycopersicum	11	Illumina PacBio	[77]
	黄瓜Cucumis sativus	11	PacBio	[64]
	番茄Solanum lycopersicum	31	PacBio HiFi	[52]
	亚洲栽培稻和非洲栽培稻 Oryza sativa and Oryza glaberrima	33	PacBio	[44]
	亚洲栽培稻、非洲栽培稻、普通野生稻和短舌野生稻 Oryza sativa, Oryza glaberrima, Oryza rufipogon and Oryza barthii	251	Nanopore	[46]
	柑橘Citrus reticulata	12	Illumina HiSeq PacBio	[62]
	鹰嘴豆Cicer arietinum	8	Illumina HiSeq	[60]
	葡萄Vitis vinifera	9	Illumina HiSeq PacBio	[59]
迭代组装 Iterative assembly	无油樟Amborella trichopoda	11	Illumina HiSeq	[66]
迭代组装 Iterative assembly	栽培和野生大豆 Glycine max and Glycine soja	1110	Illumina HiSeq	[22]

Table 2

Fig. 1

Fig. 2

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