Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa

被引：4

作者：

He, Fei ^{[1
]}

Chen, Shuai ^{[2
]}

Zhang, Yangyang ^{[1
]}

Chai, Kun ^{[2
]}

Zhang, Qing ^{[3
]}

Kong, Weilong ^{[2
]}

Qu, Shenyang ^{[2
]}

Chen, Lin ^{[1
]}

Zhang, Fan ^{[1
]}

Li, Mingna ^{[1
]}

Wang, Xue ^{[1
]}

Lv, Huigang ^{[1
]}

Zhang, Tiejun ^{[4
]}

He, Xiaofan ^{[4
]}

Li, Xiao ^{[4
]}

Li, Yajing ^{[1
]}

Li, Xianyang ^{[1
]}

Jiang, Xueqian ^{[1
]}

Xu, Ming ^{[1
]}

Sod, Bilig ^{[1
]}

Kang, Junmei ^{[1
]}

Zhang, Xingtan ^{[2
]}

Long, Ruicai ^{[1
]}

Yang, Qingchuan ^{[1
]}

机构：

[1] Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China

[2] Chinese Acad Agr Sci, Natl Key Lab Trop Crop Breeding, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr,Agr Genom Inst Shenzhe, Shenzhen 518120, Peoples R China

[3] Guangxi Univ, Coll Agr, Guangxi Key Lab Sugarcane Biol, State Key Lab Conservat & Utilizat Subtrop Agrobio, Nanning, Peoples R China

[4] Beijing Forestry Univ, Sch Grassland Sci, Beijing, Peoples R China

来源：

NATURE GENETICS | 2025年 / 57卷 / 05期

关键词：

GIBBERELLIN; 3-OXIDASE; STRUCTURAL VARIATIONS; VARIANT; GROWTH; IDENTIFICATION; PREDICTION; ALIGNMENT; GENETICS; ACCURATE; SEQUENCE;

D O I：

10.1038/s41588-025-02164-8

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Alfalfa (Medicago sativa L.), a globally important forage crop, is valued for its high nutritional quality and nitrogen-fixing capacity. Here, we present a high-quality pan-genome constructed from 24 diverse alfalfa accessions, encompassing a wide range of genetic backgrounds. This comprehensive analysis identified 433,765 structural variations and characterized 54,002 pan-gene families, highlighting the pivotal role of genomic diversity in alfalfa domestication and adaptation. Key structural variations associated with salt tolerance and quality traits were discovered, with functional analysis implicating genes such as MsMAP65 and MsGA3ox1. Notably, overexpression of MsGA3ox1 led to a reduced stem-leaf ratio and enhanced forage quality. The integration of genomic selection and marker-assisted breeding strategies improved genomic estimated breeding values across multiple traits, offering valuable genomic resources for advancing alfalfa breeding. These findings provide insights into the genetic basis of important agronomic traits and establish a solid foundation for future crop improvement.

引用

页码：1262 / 1273

页数：25

共 87 条

[1]

Abramoff M D., 2004, Biophoton. Int, V11, P36

[2] Enhancements to the ADMIXTURE algorithm for individual ancestry estimation [J].

Alexander, David H. ;

Lange, Kenneth .

BMC BIOINFORMATICS, 2011, 12

[3] Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing [J].

Alonge, Michael ;

Lebeigle, Ludivine ;

Kirsche, Melanie ;

Jenike, Katie ;

Ou, Shujun ;

Aganezov, Sergey ;

Wang, Xingang ;

Lippman, Zachary B. ;

Schatz, Michael C. ;

Soyk, Sebastian .

GENOME BIOLOGY, 2022, 23 (01)

[4] Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato [J].

Alonge, Michael ;

Wang, Xingang ;

Benoit, Matthias ;

Soyk, Sebastian ;

Pereira, Lara ;

Zhang, Lei ;

Suresh, Hamsini ;

Ramakrishnan, Srividya ;

Maumus, Florian ;

Ciren, Danielle ;

Levy, Yuval ;

Harel, Tom Hai ;

Shalev-Schlosser, Gili ;

Amsellem, Ziva ;

Razifard, Hamid ;

Caicedo, Ana L. ;

Tieman, Denise M. ;

Klee, Harry ;

Kirsche, Melanie ;

Aganezov, Sergey ;

Ranallo-Benavidez, T. Rhyker ;

Lemmon, Zachary H. ;

Kim, Jennifer ;

Robitaille, Gina ;

Kramer, Melissa ;

Goodwin, Sara ;

McCombie, W. Richard ;

Hutton, Samuel ;

Van Eck, Joyce ;

Gillis, Jesse ;

Eshed, Yuval ;

Sedlazeck, Fritz J. ;

van der Knaap, Esther ;

Schatz, Michael C. ;

Lippman, Zachary B. .

CELL, 2020, 182 (01) :145-+

[5] Goodbye reference, hello genome graphs [J].

Ameur, Adam .

NATURE BIOTECHNOLOGY, 2019, 37 (08) :866-868

[6] Achievements and Challenges in Improving Temperate Perennial Forage Legumes [J].

Annicchiarico, Paolo ;

Barrett, Brent ;

Brummer, E. Charles ;

Julier, Bernadette ;

Marshall, Athole H. .

CRITICAL REVIEWS IN PLANT SCIENCES, 2015, 34 (1-3) :327-380

[7]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkh121, 10.1093/nar/gkr1065, 10.1093/nar/gkp985]

[8] BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP plus and AUGUSTUS supported by a protein database [J].

Bruna, Tomas ;

Hoff, Katharina J. ;

Lomsadze, Alexandre ;

Stanke, Mario ;

Borodovsky, Mark .

NAR GENOMICS AND BIOINFORMATICS, 2021, 3 (01) :1-11

[9] eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale [J].

Cantalapiedra, Carlos P. ;

Hernandez-Plaza, Ana ;

Letunic, Ivica ;

Bork, Peer ;

Huerta-Cepas, Jaime .

MOLECULAR BIOLOGY AND EVOLUTION, 2021, 38 (12) :5825-5829

[10] Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa [J].

Chen, Haitao ;

Zeng, Yan ;

Yang, Yongzhi ;

Huang, Lingli ;

Tang, Bolin ;

Zhang, He ;

Hao, Fei ;

Li, Wei ;

Li, Youhan ;

Liu, Yanbin ;

Zhang, Xiaoshuang ;

Zhang, Ru ;

Zhang, Yesheng ;

Li, Yongxin ;

Wang, Kun ;

He, Hua ;

Wang, Zhongkai ;

Fan, Guangyi ;

Yang, Hui ;

Bao, Aike ;

Shang, Zhanhuan ;

Chen, Jianghua ;

Wang, Wen ;

Qiu, Qiang .

NATURE COMMUNICATIONS, 2020, 11 (01)

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