作物泛基因组研究进展与展望

doi:10.3864/j.issn.0578-1752.2025.11.001

中国农业科学 ›› 2025, Vol. 58 ›› Issue (11): 2045-2061.doi: 10.3864/j.issn.0578-1752.2025.11.001

• 作物遗传育种·种质资源·分子遗传学 • 下一篇

作物泛基因组研究进展与展望

王晖¹(), 丁保朋²(), 李彧贤², 任泉如², 周海¹, 赵均良¹^,³(), 胡海飞³()

¹ 华南农业大学生命科学学院，广州 510640
² 山西大同大学/煤基生态碳汇技术教育部工程研究中心，山西大同 037009
³ 广东省农业科学院水稻研究所/农业农村部华南优质稻遗传育种重点实验室（部省共建）/广东省水稻科学技术重点实验室/广东省水稻工程实验室，广州 510640

收稿日期:2024-11-18 接受日期:2025-01-16 出版日期:2025-06-01 发布日期:2025-06-09
通信作者:
丁保朋，E-mail：dingbp@sxdtdx.edu.cn。
赵均良，E-mail：zhaojunliang@gdaas.cn。
胡海飞，E-mail：huhaifei@gdaas.cn
联系方式: 王晖，E-mail：2224168009@qq.com。
基金资助:
国家自然科学基金青年基金(32400512); 国家自然科学基金青年基金(32102364); 广东省自然科学基金(2024A1515011981); 广东省农业科学院青年骨干人才计划(R2023YJ-QC001); 山西省高等学校青年学术带头人(2024Q031); 广东省水稻科学技术重点实验室(2023B1212060042)

Research Progress and Prospects on Crop Pan-Genomics

WANG Hui¹(), DING BaoPeng²(), LI YuXian², REN QuanRu², ZHOU Hai¹, ZHAO JunLiang¹^,³(), HU HaiFei³()

¹ College of Life Sciences, South China Agricultural University, Guangzhou 510640
² Shanxi Datong University/Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Datong 037009, Shanxi
³ Rice Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640

Received:2024-11-18 Accepted:2025-01-16 Published:2025-06-01 Online:2025-06-09

摘要/Abstract

摘要：

全球人口的持续增长和气候变化给粮食供给带来了严峻挑战，粮食安全问题因此愈发突出。为了满足不断增长的人口对粮食的需求，提升作物产量并增强其对环境的适应性已成为农业领域的重要目标。在此背景下，基因组学被视为加速作物育种进程的重要手段。通过深入挖掘和利用作物优异功能基因信息，不仅能有效提高作物产量，还能增强其抗逆性和适应性，为保障全球粮食安全和实现农业可持续发展提供有力支撑。然而，传统的单一参考基因组往往无法全面反映作物在驯化和改良过程中所累积的所有基因组变异，导致研究者对功能基因及其调控网络的认识存在局限。随着高通量测序技术的不断发展，基因组学研究开始迈入泛基因组学时代。通过整合多个高质量基因组，构建涵盖物种基因序列全集的泛基因组，能精准地鉴定包括单核苷酸多态性（SNPs）及结构变异（SVs）在内的多种遗传变异，全面地捕获物种在不同品种、亚种及野生亲缘种中广泛存在的遗传多样性，为系统挖掘优异功能基因提供更完善的分析框架。通过结合多组学数据（如转录组、蛋白质组、表观组等），泛基因组研究能在更精细的水平上挖掘优异功能基因，进而为分子育种提供更具针对性和准确性的基因靶标。同时，借助CRISPR-Cas9等基因编辑技术，可进一步对重要基因位点进行定向改造，剔除影响作物生长的不利性状或强化其对环境胁迫的抗性，从而为培育兼具高产、优质和抗逆特性的新一代作物品种奠定坚实基础。本文阐述了目前泛基因组的主要构建方法及展现形式的研究进展，并系统地梳理了作物泛基因组的发展及其在育种改良中的应用，深入探讨了泛基因组在未来作物育种中面临的挑战，对如何更好地应用泛基因组进行作物遗传改良进行了讨论，为未来精准分子育种改良提供了新的思路和策略。

关键词: 分子育种, 泛基因组, 结构变异, 新质生产力, 遗传多样性

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

王晖, 丁保朋, 李彧贤, 任泉如, 周海, 赵均良, 胡海飞. 作物泛基因组研究进展与展望[J]. 中国农业科学, 2025, 58(11): 2045-2061.

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.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.11.001

https://www.chinaagrisci.com/CN/Y2025/V58/I11/2045

图/表 4

表1

基因组测序、组装技术的发展及应用"

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

表1

表2

当今重要植物和作物泛基因组研究的概述"

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]

表2

图1

图2

参考文献 106

[1]	RAY D K, MUELLER N D, WEST P C, FOLEY J A. Yield trends are insufficient to double global crop production by 2050. PLoS ONE, 2013, 8(6): e66428.
[2]	MILLS G, SHARPS K, SIMPSON D, PLEIJEL H, FREI M, BURKEY K, EMBERSON L, UDDLING J, BROBERG M, FENG Z Z, KOBAYASHI K, AGRAWAL M. Closing the global ozone yield gap: Quantification and cobenefits for multistress tolerance. Global Change Biology, 2018, 24(10): 4869-4893. doi: 10.1111/gcb.14381 pmid: 30084165
[3]	VELÁSQUEZ A C, CASTROVERDE C D M, HE S Y. Plant- pathogen warfare under changing climate conditions. Current Biology, 2018, 28(10): R619-R634.
[4]	PROJECT I R G S. The map-based sequence of the rice genome. Nature, 2005, 436(7052): 793-800.
[5]	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. 生物技术通报, 2024, 40(10): 9-18. doi: 10.13560/j.cnki.biotech.bull.1985.2024-0669
	HE W C, XU Q, QIAN Q, SHANG L G. Development and prospects of rice pan-genomics: Important tools and applications. Biotechnology Bulletin, 2024, 40(10): 9-18. (in Chinese)
[6]	BAYER P E, GOLICZ A A, SCHEBEN A, BATLEY J, EDWARDS D. Plant pan-genomes are the new reference. Nature Plants, 2020, 6(8): 914-920. doi: 10.1038/s41477-020-0733-0 pmid: 32690893
[7]	刘羽诚, 申妍婷, 田志喜. 大豆泛基因组研究进展. 遗传, 2024, 46(3): 183-198.
	LIU Y C, SHEN Y T, TIAN Z X. Frontiers of soybean pan-genome studies. Hereditas (Beijing), 2024, 46(3): 183-198. (in Chinese)
[8]	HENDERSON I R, BOMBLIES K. Evolution and plasticity of genome-wide meiotic recombination rates. Annual Review of Genetics, 2021, 55: 23-43. doi: 10.1146/annurev-genet-021721-033821 pmid: 34310193
[9]	SAM Y. Genomic rearrangements and the evolution of clusters of locally adaptive loci. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(19): E1743-E1751.
[10]	郝晨路, 於晓芬, 曲明昊, 赖恩惠, 郭素敏, 高磊. 植物泛基因组研究进展与展望. 植物科学学报, 2022, 40(1): 124-132.
	HAO C L, YU X F, QU M H, LAI E H, GUO S M, GAO L. Current status and prospects of pan-genome studies in plants. Plant Science Journal, 2022, 40(1): 124-132. (in Chinese)
[11]	SANGER F, NICKLEN S, COULSON A R. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 1977, 74(12): 5463-5467.
[12]	VISENDI P, BERKMAN P J, HAYASHI S, GOLICZ A A, BAYER P E, RUPERAO P, HURGOBIN B, MONTENEGRO J, CHAN C K, STAŇKOVÁ H, BATLEY J, ŠIMKOVÁ H, DOLEŽEL J, EDWARDS D. An efficient approach to BAC based assembly of complex genomes. Plant Methods, 2016, 12: 2. doi: 10.1186/s13007-016-0107-9 pmid: 26793268
[13]	PATERSON A H, BOWERS J E, BRUGGMANN R, DUBCHAK I, GRIMWOOD J, GUNDLACH H, HABERER G, HELLSTEN U, MITROS T, POLIAKOV A, et al. The Sorghum bicolor genome and the diversification of grasses. Nature, 2009, 457(7229): 551-556.
[14]	SCHNABLE P S, WARE D, FULTON R S, STEIN J C, WEI F S, PASTERNAK S, LIANG C Z, ZHANG J W, FULTON L, GRAVES T A, et al. The B73 maize genome: Complexity, diversity, and dynamics. Science, 2009, 326(5956): 1112-1115. doi: 10.1126/science.1178534 pmid: 19965430
[15]	LEVY S E, MYERS R M. Advancements in next-generation sequencing. Annual Review of Genomics and Human Genetics, 2016, 17: 95-115. doi: 10.1146/annurev-genom-083115-022413 pmid: 27362342
[16]	PARITOSH K, YADAVA S K, SINGH P, BHAYANA L, MUKHOPADHYAY A, GUPTA V, BISHT N C, ZHANG J W, KUDRNA D A, COPETTI D, WING R A, LACHAGARI V B R, PRADHAN A K, PENTAL D. A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnology Journal, 2021, 19(3): 602-614.
[17]	REYES-CHIN-WO S, WANG Z W, YANG X H, KOZIK A, ARIKIT S, SONG C, XIA L F, FROENICKE L, LAVELLE D O, TRUCO M J, XIA R, ZHU S L, XU C Y, XU H Q, XU X, COX K, KORF I, MEYERS B C, MICHELMORE R W. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nature Communications, 2017, 8: 14953.
[18]	CHALHOUB B, DENOEUD F, LIU S Y, PARKIN I A P, TANG H B, WANG X Y, CHIQUET J, BELCRAM H, TONG C B, SAMANS B, et al. Plant genetics. Early allopolyploid evolution in the post- Neolithic Brassica napus oilseed genome. Science, 2014, 345(6199): 950-953.
[19]	KIM M Y, LEE S, VAN K, KIM T H, JEONG S C, CHOI I Y, KIM D S, LEE Y S, PARK D, MA J X, et al. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(51): 22032-22037.
[20]	LV Q M, LI W G, SUN Z Z, OUYANG N, JING X, HE Q, WU J, ZHENG J K, ZHENG J T, TANG S Q, et al. Resequencing of 1, 143 indica rice accessions reveals important genetic variations and different heterosis patterns. Nature Communications, 2020, 11(1): 4778.
[21]	HAO C Y, JIAO C Z, HOU J, LI T, LIU H X, WANG Y Q, ZHENG J, LIU H, BI Z H, XU F F, ZHAO J, MA L, WANG Y M, MAJEED U, LIU X, APPELS R, MACCAFERRI M, TUBEROSA R, LU H F, ZHANG X Y. Resequencing of 145 landmark cultivars reveals asymmetric sub-genome selection and strong founder genotype effects on wheat breeding in China. Molecular Plant, 2020, 13(12): 1733-1751. doi: 10.1016/j.molp.2020.09.001 pmid: 32896642
[22]	BAYER P E, VALLIYODAN B, HU H F, MARSH J I, YUAN Y X, VUONG T D, PATIL G, SONG Q J, BATLEY J, VARSHNEY R K, LAM H M, EDWARDS D, NGUYEN H T. Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome, 2022, 15(1): e20109.
[23]	VAN DIJK E L, JASZCZYSZYN Y, NAQUIN D, THERMES C. The third revolution in sequencing technology. Trends in Genetics, 2018, 34(9): 666-681. doi: S0168-9525(18)30096-9 pmid: 29941292
[24]	BELSER C, ISTACE B, DENIS E, DUBARRY M, BAURENS F C, FALENTIN C, GENETE M, BERRABAH W, CHÈVRE A M, DELOURME R, et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature Plants, 2018, 4(11): 879-887. doi: 10.1038/s41477-018-0289-4 pmid: 30390080
[25]	JIAO Y P, PELUSO P, SHI J H, LIANG T, STITZER M C, WANG B, CAMPBELL M S, STEIN J C, WEI X H, CHIN C S, et al. Improved maize reference genome with single-molecule technologies. Nature, 2017, 546(7659): 524-527.
[26]	CHENG H Y, CONCEPCION G T, FENG X W, ZHANG H W, LI H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods, 2021, 18(2): 170-175.
[27]	ATHIYANNAN N, ABROUK M, BOSHOFF W H P, CAUET S, RODDE N, KUDRNA D, MOHAMMED N, BETTGENHAEUSER J, BOTHA K S, DERMAN S S, WING R A, PRINS R, KRATTINGER S G. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nature Genetics, 2022, 54(3): 227-231. doi: 10.1038/s41588-022-01022-1 pmid: 35288708
[28]	TANG D, JIA Y X, ZHANG J Z, LI H B, CHENG L, WANG P, BAO Z G, LIU Z H, FENG S S, ZHU X J, LI D W, ZHU G T, WANG H R, ZHOU Y, ZHOU Y F, BRYAN G J, ROBIN BUELL C, ZHANG C Z, HUANG S W. Genome evolution and diversity of wild and cultivated potatoes. Nature, 2022, 606(7914): 535-541.
[29]	KARST S M, ZIELS R M, KIRKEGAARD R H, SØRENSEN E A, MCDONALD D, ZHU Q Y, KNIGHT R, ALBERTSEN M. High- accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nature Methods, 2021, 18(2): 165-169.
[30]	KOREN S, WALENZ B P, BERLIN K, MILLER J R, BERGMAN N H, PHILLIPPY A M. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 2017, 27(5): 722-736.
[31]	FREIRE B, LADRA S, PARAMA J R. Memory-efficient assembly using flye. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022, 19(6): 3564-3577.
[32]	HU J, WANG Z, SUN Z Y, HU B X, AYOOLA A O, LIANG F, LI J J, SANDOVAL J R, COOPER D N, YE K, RUAN J, XIAO C L, WANG D P, WU D D, WANG S. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology, 2024, 25(1): 107. doi: 10.1186/s13059-024-03252-4 pmid: 38671502
[33]	CHOI J Y, LYE Z N, GROEN S C, DAI X G, RUGHANI P, ZAAIJER S, HARRINGTON E D, JUUL S, PURUGGANAN M D. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biology, 2020, 21(1): 21. doi: 10.1186/s13059-020-1938-2 pmid: 32019604
[34]	SALSON M, ORJUELA J, MARIAC C, ZEKRAOUÏ L, COUDERC M, ARRIBAT S, RODDE N, FAYE A, KANE N A, TRANCHANT- DUBREUIL C, VIGOUROUX Y, BERTHOULY-SALAZAR C. An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping. G3, 2023, 13(5): jkad051.
[35]	NURK S, KOREN S, RHIE A, RAUTIAINEN M, BZIKADZE A V, MIKHEENKO A, VOLLGER M R, ALTEMOSE N, URALSKY L, GERSHMAN A, et al. The complete sequence of a human genome. Science, 2022, 376(6588): 44-53. doi: 10.1126/science.abj6987 pmid: 35357919
[36]	CHEN J, WANG Z J, TAN K W, HUANG W, SHI J P, LI T, HU J, WANG K, WANG C, XIN B B, ZHAO H M, SONG W B, HUFFORD M B, SCHNABLE J C, JIN W W, LAI J S. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics, 2023, 55(7): 1221-1231. doi: 10.1038/s41588-023-01419-6 pmid: 37322109
[37]	BAO J D, ZHANG H, WANG F L, LI L, ZHU X M, XU J F, WANG Y, LIU Z J, ZHAI G W, XU H, LIN F C, ZHU Y. Telomere-to- telomere genome assemblies of two Chinese Baijiu-brewing Sorghum landraces. Plant Communications, 2024, 5(6): 100933.
[38]	SHIZUYA H, BIRREN B, KIM U J, MANCINO V, SLEPAK T, TACHIIRI Y, SIMON M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89(18): 8794-8797.
[39]	MARDIS E R. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 2008, 9: 387-402. doi: 10.1146/annurev.genom.9.081307.164359 pmid: 18576944
[40]	MARX V. Method of the year: Long-read sequencing. Nature Methods, 2023, 20(1): 6-11. doi: 10.1038/s41592-022-01730-w pmid: 36635542
[41]	KOREN S, SCHATZ M C, WALENZ B P, MARTIN J, HOWARD J T, GANAPATHY G, WANG Z, RASKO D A, RICHARD MCCOMBIE W, JARVIS E D, PHILLIPPY A M. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 2012, 30(7): 693-700.
[42]	ZAPATA L, DING J, WILLING E M, HARTWIG B, BEZDAN D, JIAO W B, PATEL V, VELIKKAKAM JAMES G, KOORNNEEF M, OSSOWSKI S, SCHNEEBERGER K. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(28): E4052-E4060.
[43]	ZHOU Q, TANG D, HUANG W, YANG Z M, ZHANG Y, HAMILTON J P, VISSER R G F, BACHEM C W B, ROBIN BUELL C, ZHANG Z H, ZHANG C Z, HUANG S W. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nature Genetics, 2020, 52(10): 1018-1023. doi: 10.1038/s41588-020-0699-x pmid: 32989320
[44]	QIN P, LU H W, DU H L, WANG H, CHEN W L, CHEN Z, HE Q, OU S J, ZHANG H Y, LI X Z, HE M, YIN J J, LI T, JIANG N, CHEN X W, LIANG C Z, LI S G. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell, 2021, 184(13): 3542-3558.e16. doi: 10.1016/j.cell.2021.04.046 pmid: 34051138
[45]	SCHATZ M C, MARON L G, STEIN J C, HERNANDEZ WENCES A, GURTOWSKI J, BIGGERS E, LEE H Y, KRAMER M, ANTONIOU E, GHIBAN E, WRIGHT M H, CHIA J M, WARE D, MCCOUCH S R, MCCOMBIE W R. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology, 2014, 15(11): 506.
[46]	SHANG L G, LI X X, HE H Y, YUAN Q L, SONG Y N, WEI Z R, LIN H, HU M, ZHAO F L, ZHANG C, et al. A super pan-genomic landscape of rice. Cell Research, 2022, 32(10): 878-896. doi: 10.1038/s41422-022-00685-z pmid: 35821092
[47]	ZHANG F, XUE H Z, DONG X R, LI M, ZHENG X M, LI Z K, XU J L, WANG W S, WEI C C. Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Research, 2022, 32(5): 853-863. doi: 10.1101/gr.276015.121 pmid: 35396275
[48]	WU S, SUN H H, GAO L, BRANHAM S, MCGREGOR C, RENNER S S, XU Y, KOUSIK C, WECHTER W P, LEVI A, FEI Z J. A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnology Journal, 2023, 21(10): 1926-1928.
[49]	ZHANG Y L, ZHAO M X, TAN J S, HUANG M H, CHU X, LI Y, HAN X, FANG T H, TIAN Y, JARRET R, LU D D, CHEN Y J, XUE L F, LI X N, QIN G C, LI B S, SUN Y D, DENG X W, DENG Y, ZHANG X P, HE H. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics, 2024, 56(8): 1750-1761.
[50]	SUN Y, KOU D R, LI Y, NI J P, WANG J, ZHANG Y M, WANG Q N, JIANG B, WANG X, SUN Y X, XU X T, TAN X J, ZHANG Y J, KONG X D. Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection. BMC Genomics, 2023, 24(1): 332.
[51]	BOZAN I, ACHAKKAGARI S R, ANGLIN N L, ELLIS D, TAI H H, STRÖMVIK M V. Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species. Proceedings of the National Academy of Sciences of the United States of America, 2023, 120(31): e2211117120.
[52]	ZHOU Y, ZHANG Z Y, BAO Z G, LI H B, LYU Y Q, ZAN Y J, WU Y Y, CHENG L, FANG Y H, WU K, ZHANG J Z, LYU H J, LIN T, GAO Q, SAHA S, MUELLER L, FEI Z J, STÄDLER T, XU S Z, ZHANG Z W, SPEED D, HUANG S W. Graph pangenome captures missing heritability and empowers tomato breeding. Nature, 2022, 606(7914): 527-534.
[53]	HUFFORD M B, SEETHARAM A S, WOODHOUSE M R, CHOUGULE K M, OU S J, LIU J N, RICCI W A, GUO T T, OLSON A, QIU Y J, et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 2021, 373(6555): 655-662.
[54]	SONG J M, GUAN Z L, HU J L, GUO C C, YANG Z Q, WANG S, LIU D X, WANG B, LU S P, ZHOU R, XIE W Z, CHENG Y F, ZHANG Y T, LIU K D, YANG Q Y, CHEN L L, GUO L. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 2020, 6(1): 34-45.
[55]	JAYAKODI M, PADMARASU S, HABERER G, BONTHALA V S, GUNDLACH H, MONAT C, LUX T, KAMAL N, LANG D, HIMMELBACH A, et al. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature, 2020, 588(7837): 284-289.
[56]	HE X, QI Z Y, LIU Z P, CHANG X, ZHANG X L, LI J Y, WANG M J. Pangenome analysis reveals transposon-driven genome evolution in cotton. BMC Biology, 2024, 22(1): 92. doi: 10.1186/s12915-024-01893-2 pmid: 38654264
[57]	ZHAO X B, YU J Y, CHANDA B, ZHAO J T, WU S, ZHENG Y, SUN H H, LEVI A, LING K S, FEI Z J. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. New Phytologist, 2024, 242(5): 2285-2300.
[58]	DING B P, HU H F, CAO Y P, XU R R, LIN Y J, MUHAMMAD T U Q, SONG Y Q, HE G Q, HAN Y Z, GUO H P, QIAO J, ZHAO J G, FENG X X, YANG S, GUO X H, VARSHNEY R K, LI L L. Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation. Horticultural Plant Journal, 2024, 10(6): 1274-1290.
[59]	COCHETEL N, MINIO A, GUARRACINO A, GARCIA J F, FIGUEROA-BALDERAS R, MASSONNET M, KASUGA T, LONDO J P, GARRISON E, GAUT B S, CANTU D. A super- pangenome of the North American wild grape species. Genome Biology, 2023, 24(1): 290.
[60]	KHAN A W, GARG V, SUN S, GUPTA S, DUDCHENKO O, ROORKIWAL M, CHITIKINENI A, BAYER P E, SHI C C, UPADHYAYA H D, et al. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics, 2024, 56(6): 1225-1234.
[61]	YAN H D, SUN M, ZHANG Z R, JIN Y R, ZHANG A L, LIN C, WU B C, HE M, XU B, WANG J, et al. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nature Genetics, 2023, 55(3): 507-518. doi: 10.1038/s41588-023-01302-4 pmid: 36864101
[62]	HUANG Y, HE J X, XU Y T, ZHENG W K, WANG S H, CHEN P, ZENG B, YANG S Z, JIANG X L, LIU Z S, et al. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in Citrus fruits. Nature Genetics, 2023, 55(11): 1964-1975.
[63]	SHI T T, ZHANG X X, HOU Y K, JIA C F, DAN X M, ZHANG Y L, JIANG Y Z, LAI Q, FENG J J, FENG J J, et al. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Molecular Plant, 2024, 17(5): 725-746.
[64]	LI H B, WANG S H, CHAI S, YANG Z Q, ZHANG Q Q, XIN H J, XU Y C, LIN S N, CHEN X X, YAO Z W, YANG Q Y, FEI Z J, HUANG S W, ZHANG Z H. Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nature Communications, 2022, 13(1): 682. doi: 10.1038/s41467-022-28362-0 pmid: 35115520
[65]	BEAULIEU C, LIBOUREL C, ZAMAR D L M, EL MAHBOUBI K, HOEY D J, KELLER J, GIROU C, CLEMENTE H S, DIOP I, AMBLARD E, et al. The Marchantia pangenome reveals ancient mechanisms of plant adaptation to the environment. bioRxiv, 2023.
[66]	HU H F, SCHEBEN A, VERPAALEN B, TIRNAZ S, BAYER P E, HODEL R G J, BATLEY J, SOLTIS D E, SOLTIS P S, EDWARDS D. Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist, 2022, 233(4): 1548-1555.
[67]	GUO N, WANG S Y, WANG T Y, DUAN M M, ZONG M, MIAO L M, HAN S, WANG G X, LIU X, ZHANG D S, JIAO C Z, XU H W, CHEN L Y, FEI Z J, LI J B, LIU F. A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. Plant Communications, 2024, 5(2): 100791.
[68]	LI Y H, ZHOU G Y, MA J X, JIANG W K, JIN L G, ZHANG Z H, GUO Y, ZHANG J B, SUI Y, ZHENG L T, et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 2014, 32(10): 1045-1052.
[69]	YANG J H, LIU D Y, WANG X W, JI C M, CHENG F, LIU B N, HU Z Y, CHEN S, PENTAL D, JU Y H, et al. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nature Genetics, 2016, 48(10): 1225-1232.
[70]	JIAO C Z, XIE X M, HAO C Y, CHEN L Y, XIE Y X, GARG V, ZHAO L, WANG Z H, ZHANG Y Q, LI T, et al. Pan-genome bridges wheat structural variations with habitat and breeding. Nature, 2025, 637: 384-393.
[71]	SHEPARD S S, MENO S, BAHL J, WILSON M M, BARNES J, NEUHAUS E. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics, 2016, 17(1): 708.
[72]	WANG W S, MAULEON R, HU Z Q, CHEBOTAROV D, TAI S S, WU Z C, LI M, ZHENG T Q, FUENTES R R, ZHANG F, et al. Genomic variation in 3, 010 diverse accessions of Asian cultivated rice. Nature, 2018, 557(7703): 43-49.
[73]	GAO L, GONDA I, SUN H H, MA Q Y, BAO K, TIEMAN D M, BURZYNSKI-CHANG E A, FISH T L, STROMBERG K A, SACKS G L, et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 2019, 51(6): 1044-1051. doi: 10.1038/s41588-019-0410-2 pmid: 31086351
[74]	LYU X L, XIA Y L, WANG C H, ZHANG K J, DENG G C, SHEN Q H, GAO W, ZHANG M Y, LIAO N Q, LING J, BO Y M, HU Z Y, YANG J H, ZHANG M F. Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops. Plant Physiology, 2023, 193(2): 1330-1348. doi: 10.1093/plphys/kiad405 pmid: 37477947
[75]	GUI S T, WEI W J, JIANG C L, LUO J Y, CHEN L, WU S S, LI W Q, WANG Y B, LI S Y, YANG N, LI Q, FERNIE A R, YAN J B. A pan-Zea genome map for enhancing maize improvement. Genome Biology, 2022, 23(1): 178.
[76]	EDWARDS D, BATLEY J. Graph pangenomes find missing heritability. Nature Genetics, 2022, 54(7): 919-920.
[77]	LI N, HE Q, WANG J, WANG B K, ZHAO J T, HUANG S Y, YANG T, TANG Y P, YANG S B, AISIMUTUOLA P, et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics, 2023, 55(5): 852-860. doi: 10.1038/s41588-023-01340-y pmid: 37024581
[78]	JAYAKODI M, LU Q X, PIDON H, TIMOTHY RABANUS-WALLACE M, BAYER M, LUX T, GUO Y, JAEGLE B, BADEA A, BEKELE W, et al. Structural variation in the pangenome of wild and domesticated barley. Nature, 2024, 636(8043): 654-662.
[79]	WANG B B, HOU M, SHI J P, KU L X, SONG W, LI C H, NING Q, LI X, LI C Y, ZHAO B B, et al. De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nature Genetics, 2023, 55(2): 312-323.
[80]	LIU Y C, DU H L, LI P C, SHEN Y T, PENG H, LIU S L, ZHOU G A, ZHANG H K, LIU Z, SHI M, HUANG X H, LI Y, ZHANG M, WANG Z, ZHU B G, HAN B, LIANG C Z, TIAN Z X. Pan-genome of wild and cultivated soybeans. Cell, 2020, 182(1): 162-176.e13. doi: S0092-8674(20)30618-8 pmid: 32553274
[81]	HE Q, TANG S, ZHI H, CHEN J F, ZHANG J, LIANG H K, ALAM O, LI H B, ZHANG H, XING L H, et al. A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics, 2023, 55(7): 1232-1242.
[82]	HU H F, LI R S, ZHAO J L, BATLEY J, EDWARDS D. Technological development and advances for constructing and analyzing plant pangenomes. Genome Biology and Evolution, 2024, 16(4): evae081.
[83]	GARRISON E, SIRÉN J, NOVAK A M, HICKEY G, EIZENGA J M, DAWSON E T, JONES W, GARG S, MARKELLO C, LIN M F, PATEN B, DURBIN R. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 2018, 36(9): 875-879. doi: 10.1038/nbt.4227 pmid: 30125266
[84]	LI H, FENG X W, CHU C. The design and construction of reference pangenome graphs with minigraph. Genome Biology, 2020, 21(1): 265. doi: 10.1186/s13059-020-02168-z pmid: 33066802
[85]	HICKEY G, MONLONG J, EBLER J, NOVAK A M, EIZENGA J M, GAO Y, CONSORTIUM H P R, MARSCHALL T, LI H, PATEN B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology, 2024, 42(4): 663-673.
[86]	GARRISON E, GUARRACINO A, HEUMOS S, VILLANI F, BAO Z, TATTINI L, HAGMANN J, VORBRUGG S, MARCO-SOLA S, KUBICA C, et al. Building pangenome graphs. Nature Methods, 2024, 21(11): 2008-2012. doi: 10.1038/s41592-024-02430-3 pmid: 39433878
[87]	王英豪, 余嘉鑫, 唐海宝, 张兴坦. 植物复杂基因组与泛基因组研究现状与展望. 中国科学: 生命科学, 2024, 54(2): 233-246.
	WANG Y H, YU J X, TANG H B, ZHANG X T. Research status and prospect of plant complex genomes and pan-genomes. Scientia Sinica (Vitae), 2024, 54(2): 233-246. (in Chinese)
[88]	ZHANG H Y, MITTAL N, LEAMY L J, BARAZANI O, SONG B H. Back into the wild: Apply untapped genetic diversity of wild relatives for crop improvement. Evolutionary Applications, 2017, 10(1): 5-24.
[89]	MOHD SAAD N S, NEIK T X, THOMAS W J W, AMAS J C, CANTILA A Y, CRAIG R J, EDWARDS D, BATLEY J. Advancing designer crops for climate resilience through an integrated genomics approach. Current Opinion in Plant Biology, 2022, 67: 102220.
[90]	HU H F, ZHAO J L, THOMAS W J W, BATLEY J, EDWARDS D. The role of pangenomics in orphan crop improvement. Nature Communications, 2025, 16(1): 118.
[91]	DELLA COLETTA R, QIU Y J, OU S J, HUFFORD M B, HIRSCH C N. How the pan-genome is changing crop genomics and improvement. Genome Biology, 2021, 22(1): 3. doi: 10.1186/s13059-020-02224-8 pmid: 33397434
[92]	ALONGE M, WANG X G, BENOIT M, SOYK S, PEREIRA L, ZHANG L, SURESH H, RAMAKRISHNAN S, MAUMUS F, CIREN D, et al. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell, 2020, 182(1): 145-161.e23. doi: S0092-8674(20)30616-4 pmid: 32553272
[93]	LI Q, FENG Q, SNOUFFER A, ZHANG B Y, RODRÍGUEZ G R, VAN DER KNAAP E. Increasing fruit weight by editing a Cis- regulatory element in tomato KLUH promoter using CRISPR/Cas9. Frontiers in Plant Science, 2022, 13: 879642.
[94]	YU H, LIN T, MENG X B, DU H L, ZHANG J K, LIU G F, CHEN M J, JING Y H, KOU L Q, LI X X, et al. A route to de novo domestication of wild allotetraploid rice. Cell, 2021, 184(5): 1156-1170.e14.
[95]	TAY FERNANDEZ C G, NESTOR B J, DANILEVICZ M F, MARSH J I, PETEREIT J, BAYER P E, BATLEY J, EDWARDS D. Expanding gene-editing potential in crop improvement with pangenomes. International Journal of Molecular Sciences, 2022, 23(4): 2276.
[96]	HU H F, SCHEBEN A, WANG J, LI F P, LI C D, EDWARDS D, ZHAO J L. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. Plant Biotechnology Journal, 2024, 22(3): 544-554.
[97]	GAGE J L, VAILLANCOURT B, HAMILTON J P, MANRIQUE-CARPINTERO N C, GUSTAFSON T J, BARRY K, LIPZEN A, TRACY W F, MIKEL M A, KAEPPLER S M, BUELL C R, DE LEON N. Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel. The Plant Genome, 2019, 12(2): 180069.
[98]	DAWARE A, MALIK A, SRIVASTAVA R, DAS D, ELLUR R K, SINGH A K, TYAGI A K, PARIDA S K. Rice Pangenome Genotyping Array: An efficient genotyping solution for pangenome-based accelerated genetic improvement in rice. The Plant Journal, 2023, 113(1): 26-46.
[99]	RUPERAO P, THIRUNAVUKKARASU N, GANDHAM P, SELVANAYAGAM S, GOVINDARAJ M, NEBIE B, MANYASA E, GUPTA R, DAS R R, ODENY D A, GANDHI H, EDWARDS D, DESHPANDE S P, RATHORE A. Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain. Frontiers in Plant Science, 2021, 12: 666342.
[100]	WANG J, YANG W, ZHANG S H, HU H F, YUAN Y X, DONG J F, CHEN L, MA Y M, YANG T F, ZHOU L, CHEN J S, LIU B, LI C D, EDWARDS D, ZHAO J L. A pangenome analysis pipeline provides insights into functional gene identification in rice. Genome Biology, 2023, 24(1): 19. doi: 10.1186/s13059-023-02861-9 pmid: 36703158
[101]	SIBBESEN J A, EIZENGA J M, NOVAK A M, SIRÉN J, CHANG X, GARRISON E, PATEN B. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature Methods, 2023, 20(2): 239-247. doi: 10.1038/s41592-022-01731-9 pmid: 36646895
[102]	ZHANG H, CHEN W, ZHU D, ZHANG B T, XU Q, SHI C L, HE H Y, DAI X F, LI Y L, HE W C, et al. Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice. The Plant Cell, 2024, 36(10): 4372-4387.
[103]	ZHONG Y Y, LUO Y H, SUN J L, QIN X M, GAN P, ZHOU Z W, QIAN Y Q, ZHAO R P, ZHAO Z Y, CAI W G, LUO J J, CHEN L L, SONG J M. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice. The Plant Cell, 2024, 36(6): 2117-2139. doi: 10.1093/plcell/koae039 pmid: 38345423
[104]	HSIEH C H, CHANG Y S, YEN M R, HSIEH J A, CHEN P Y. Predicting protein synergistic effect in Arabidopsis using epigenome profiling. Nature Communications, 2024, 15(1): 9160.
[105]	DONG X M, ZHANG M, CHEN J, PENG L Z, ZHANG N, WANG X, LAI J S. Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm. Molecular Plant, 2017, 10(3): 442-455. doi: S1674-2052(16)30232-5 pmid: 27793787
[106]	WANG P, WU X, SHI Z B, TAO S T, LIU Z, QI K J, XIE Z H, QIAO X, GU C, YIN H, CHENG M Y, GU X Y, LIU X Y, TANG C, CAO P, XU S H, ZHOU B J, GU T T, BIAN Y Y, WU J Y, ZHANG S L. A large-scale proteogenomic atlas of pear. Molecular Plant, 2023, 16(3): 599-615. doi: 10.1016/j.molp.2023.01.011 pmid: 36733253

作物泛基因组研究进展与展望

Research Progress and Prospects on Crop Pan-Genomics

RichHTML

PDF

赞

可视化

摘要/Abstract

引用本文

使用本文

图/表 4

参考文献 106

相关文章 15

Metrics

本文评价

推荐阅读 0

[1]	唐桂梅, 李卫东, 周宇霞, 孔佑涵, 肖晓玲, 彭颖姝, 张力, 符红艳, 刘洋, 黄国林. 基于表型性状分析蕙兰种质资源遗传多样性[J]. 中国农业科学, 2025, 58(2): 339-354.
[2]	李沛, 何治霖, 谈月霞, 赵婉彤, 冯锦英, 陈贵虎, 严池, 王子豪, 黄平, 江东. 基于重测序数据与表型性状的宽皮柑橘遗传多样性分析与优异种质筛选[J]. 中国农业科学, 2024, 57(23): 4761-4773.
[3]	杨春, 杨代星, 李燕, 梁思慧, 邓小强, 乔大河, 陈娟, 郭燕, 林开勤, 陈正武. 贵州大树茶形态学特征及生化成分综合分析[J]. 中国农业科学, 2024, 57(19): 3894-3916.
[4]	李玉姗, 肖菁, 马越, 田超, 赵连佳, 王帆, 宋羽, 蒋程瑶. 169份番茄种质资源表型性状遗传多样性分析及综合评价[J]. 中国农业科学, 2024, 57(18): 3671-3683.
[5]	翟彩娇, 葛礼姣, 程玉静, 仇亮, 王小秋, 刘水东. 基于表型性状与SSR标记的冬瓜、节瓜种质资源遗传多样性分析[J]. 中国农业科学, 2024, 57(17): 3440-3457.
[6]	雷梦林, 刘霞, 王艳珍, 崔国庆, 穆志新, 刘龙龙, 李欣, 逯腊虎, 李晓丽, 张晓军. 基于55K SNP芯片的山西冬小麦种质资源遗传多样性分析[J]. 中国农业科学, 2024, 57(10): 1845-1856.
[7]	张一中, 张晓娟, 梁笃, 郭琦, 范昕琦, 聂萌恩, 王绘艳, 赵文博, 杜维俊, 柳青山. 基于表型性状的高粱育种材料遗传多样性分析及综合评价[J]. 中国农业科学, 2023, 56(15): 2837-2853.
[8]	李欢, 鄢小青, 杨占烈, 谭金玉, 黎小冰, 陈能刚, 吴荣菊, 陈惠查, 阮仁超. 贵州香禾糯地方稻种资源表型遗传多样性分析与综合评价[J]. 中国农业科学, 2023, 56(11): 2035-2046.
[9]	姜朋, 张鹏, 姚金保, 吴磊, 何漪, 李畅, 马鸿翔, 张旭. 宁麦系列小麦品种的性状特点及相关基因位点分析[J]. 中国农业科学, 2022, 55(2): 233-247.
[10]	李晓川,王朝海,周平,马维,吴瑞,宋治豪,梅艳. 马铃薯品种（系）田间晚疫病抗性评价和全基因组遗传多样性分析[J]. 中国农业科学, 2022, 55(18): 3484-3500.
[11]	万映伶,朱梦婷,刘爱青,金亦佳,刘燕. 中国观赏芍药表型多样性解析与资源评价[J]. 中国农业科学, 2022, 55(18): 3629-3639.
[12]	胡光明,张琼,韩飞,李大卫,李作洲,汪志,赵婷婷,田华,刘小莉,钟彩虹. 猕猴桃属植物通用型SSR分子标记引物的筛选及应用[J]. 中国农业科学, 2022, 55(17): 3411-3425.
[13]	王璐伟,沈志军,李贺欢,潘磊,牛良,崔国朝,曾文芳,王志强,鲁振华. 基于SSR荧光标记的79份桃种质遗传多样性分析[J]. 中国农业科学, 2022, 55(15): 3002-3017.
[14]	陈旭,郝雅琼,聂兴华,杨海莹,刘松,王雪峰,曹庆芹,秦岭,邢宇. 板栗总苞和坚果主要性状与SSR标记的关联分析[J]. 中国农业科学, 2022, 55(13): 2613-2628.
[15]	徐晓,任根增,赵欣蕊,常金华,崔江慧. 中国高粱地方品种和育成品种穗部表型性状精准鉴定及综合评价[J]. 中国农业科学, 2022, 55(11): 2092-2108.