Breeding for disease resistance in soybean: a global perspective

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Abstract

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This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world.

Abstract

Breeding disease-resistant soybean [ Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00122-022-04101-3.

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Most cited references 636

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The global burden of pathogens and pests on major food crops

Serge Savary, Laetitia Willocquet, Sarah Pethybridge … (2019)

Crop pathogens and pests reduce the yield and quality of agricultural production. They cause substantial economic losses and reduce food security at household, national and global levels. Quantitative, standardized information on crop losses is difficult to compile and compare across crops, agroecosystems and regions. Here, we report on an expert-based assessment of crop health, and provide numerical estimates of yield losses on an individual pathogen and pest basis for five major crops globally and in food security hotspots. Our results document losses associated with 137 pathogens and pests associated with wheat, rice, maize, potato and soybean worldwide. Our yield loss (range) estimates at a global level and per hotspot for wheat (21.5% (10.1-28.1%)), rice (30.0% (24.6-40.9%)), maize (22.5% (19.5-41.1%)), potato (17.2% (8.1-21.0%)) and soybean (21.4% (11.0-32.4%)) suggest that the highest losses are associated with food-deficit regions with fast-growing populations, and frequently with emerging or re-emerging pests and diseases. Our assessment highlights differences in impacts among crop pathogens and pests and among food security hotspots. This analysis contributes critical information to prioritize crop health management to improve the sustainability of agroecosystems in delivering services to societies.

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Genome sequence of the palaeopolyploid soybean.

Jeremy Schmutz, Steven Cannon, Jessica Schlueter … (2010)

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

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Top 10 plant-parasitic nematodes in molecular plant pathology.

John Jones, Annelies Haegeman, Etienne G. J. Danchin … (2013)

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly. © 2013 BSPP AND JOHN WILEY & SONS LTD.

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All references

Author and article information

Contributors

Feng Lin:

ORCID: http://orcid.org/0000-0001-7491-4444

fenglin@msu.edu

Sushil Satish Chhapekar:

ORCID: http://orcid.org/0000-0002-9802-884X

sushil.chhapekar@missouri.edu

Caio Canella Vieira:

ORCID: http://orcid.org/0000-0001-5428-3753

canellavieirac@mail.missouri.edu

Marcos Paulo Da Silva:

ORCID: http://orcid.org/0000-0002-8842-3758

mpdasilv@uark.edu

Alejandro Rojas:

ORCID: http://orcid.org/0000-0001-5492-5963

jarojas@uark.edu

Dongho Lee: leedongho@missouri.edu

Nianxi Liu:

ORCID: http://orcid.org/0000-0002-5918-4727

lnx69@126.com

Esteban Mariano Pardo:

ORCID: http://orcid.org/0000-0001-6777-0307

marianopardo@eeaoc.org.ar

Yi-Chen Lee: ylkg2@missouri.edu

Zhimin Dong: dongzhimin2005@126.com

Jose Baldin Pinheiro:

ORCID: http://orcid.org/0000-0003-1294-2081

jbaldin@usp.br

Leonardo Daniel Ploper:

ORCID: http://orcid.org/0000-0001-9032-4479

dt@eeaoc.org.ar

John Rupe: jrupe@uark.edu

Pengyin Chen: chenpe@missouri.edu

Dechun Wang:

ORCID: http://orcid.org/0000-0001-7322-7837

wangdech@msu.edu

Henry T. Nguyen:

ORCID: http://orcid.org/0000-0002-7597-1800

nguyenhenry@missouri.edu

Journal

Journal ID (nlm-ta): Theor Appl Genet

Journal ID (iso-abbrev): Theor Appl Genet

Title: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0040-5752

ISSN (Electronic): 1432-2242

Publication date (Electronic): 5 July 2022

Publication date PMC-release: 5 July 2022

Publication date (Print): 2022

Volume: 135

Issue: 11

Pages: 3773-3872

Affiliations

[1 ]GRID grid.17088.36, ISNI 0000 0001 2150 1785, Department of Plant, Soil and Microbial Sciences, , Michigan State University, ; East Lansing, MI 48824 USA

[2 ]GRID grid.134936.a, ISNI 0000 0001 2162 3504, Division of Plant Sciences and National Center for Soybean Biotechnology, , University of Missouri-Columbia, ; Columbia, MO 65211 USA

[3 ]GRID grid.134936.a, ISNI 0000 0001 2162 3504, Fisher Delta Research Center, , University of Missouri, ; Portageville, MO 63873 USA

[4 ]GRID grid.411017.2, ISNI 0000 0001 2151 0999, Department of Entomology and Plant Pathology, , University of Arkansas, ; Fayetteville, AR 72701 USA

[5 ]GRID grid.464388.5, ISNI 0000 0004 1756 0215, Soybean Research Institute, , Jilin Academy of Agricultural Sciences, ; Changchun,, 130033 Jilin China

[6 ]GRID grid.423606.5, ISNI 0000 0001 1945 2152, Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], ; Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina

[7 ]GRID grid.11899.38, ISNI 0000 0004 1937 0722, Departamento de Genética, , Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), ; PO Box 9, Piracicaba, SP 13418-900 Brazil

Author notes

Communicated by Rajeev K. Varshney.

Author information

Feng Lin http://orcid.org/0000-0001-7491-4444

Sushil Satish Chhapekar http://orcid.org/0000-0002-9802-884X

Caio Canella Vieira http://orcid.org/0000-0001-5428-3753

Marcos Paulo Da Silva http://orcid.org/0000-0002-8842-3758

Alejandro Rojas http://orcid.org/0000-0001-5492-5963

Nianxi Liu http://orcid.org/0000-0002-5918-4727

Esteban Mariano Pardo http://orcid.org/0000-0001-6777-0307

Jose Baldin Pinheiro http://orcid.org/0000-0003-1294-2081

Leonardo Daniel Ploper http://orcid.org/0000-0001-9032-4479

Dechun Wang http://orcid.org/0000-0001-7322-7837

Henry T. Nguyen http://orcid.org/0000-0002-7597-1800

Article

Publisher ID: 4101

DOI: 10.1007/s00122-022-04101-3

PMC ID: 9729162

PubMed ID: 35790543

SO-VID: e7fe5617-f69a-4717-92e4-856dd4d4ba49

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 21 November 2021

Date accepted : 11 April 2022

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100012009, United Soybean Board;

Award ID: 2120-172-0153

Award Recipient : Pengyin Chen

Funded by: Michigan Soybean Promotion Committee

Funded by: Missouri Soybean Merchandising Council

Funded by: FundRef http://dx.doi.org/10.13039/100007483, Arkansas Soybean Promotion Board;

Funded by: FundRef http://dx.doi.org/10.13039/100005825, National Institute of Food and Agriculture;

Award ID: Hatch project 1011788

Award ID: Hatch project 1017862

Award Recipient : John Rupe Dechun Wang

Funded by: FundRef http://dx.doi.org/10.13039/100011138, AgBioResearch, Michigan State University;

Award ID: MICL02013

Award Recipient : Dechun Wang

Funded by: FundRef http://dx.doi.org/10.13039/501100013061, Jilin Scientific and Technological Development Program;

Award ID: 20200201136JC

Award Recipient : Nianxi Liu

Funded by: FundRef http://dx.doi.org/10.13039/501100010031, Postdoctoral Research Foundation of China;

Award ID: 2019M661234

Award Recipient : Nianxi Liu Zhimin Dong

Funded by: FundRef http://dx.doi.org/10.13039/501100003033, Ministerio de Ciencia, Tecnología e Innovación Productiva;

Funded by: Plataforma BiotecSur-UE, Proyecto BiotecSojaSur I

Award ID: 127119

Award Recipient : Leonardo Daniel Ploper

Funded by: Estación Experimental Agroindustrial Obispo Colombres

Award ID: 2005-35332

Award Recipient : Leonardo Daniel Ploper

Funded by: FundRef http://dx.doi.org/10.13039/501100003074, Agencia Nacional de Promoción Científica y Tecnológica;

Award ID: 2016-0098

Award Recipient : Leonardo Daniel Ploper

Funded by: FundRef http://dx.doi.org/10.13039/501100011789, Department of Science and Technology of Jilin Province;

Award ID: 20200201136JC

Award Recipient : Zhimin Dong

Breeding for disease resistance in soybean: a global perspective

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Abstract

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Climate Change: Open Access

Most cited references 636

The global burden of pathogens and pests on major food crops

Genome sequence of the palaeopolyploid soybean.

Top 10 plant-parasitic nematodes in molecular plant pathology.

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