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Nissan N, Hooker J, Arezza E, Dick K, Golshani A, Mimee B, Cober E, Green J, Samanfar B. Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode. FRONTIERS IN BIOINFORMATICS 2023; 3:1199675. [PMID: 37409347 PMCID: PMC10319130 DOI: 10.3389/fbinf.2023.1199675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
The soybean cyst nematode (SCN) [Heterodera glycines Ichinohe] is a devastating pathogen of soybean [Glycine max (L.) Merr.] that is rapidly becoming a global economic issue. Two loci conferring SCN resistance have been identified in soybean, Rhg1 and Rhg4; however, they offer declining protection. Therefore, it is imperative that we identify additional mechanisms for SCN resistance. In this paper, we develop a bioinformatics pipeline to identify protein-protein interactions related to SCN resistance by data mining massive-scale datasets. The pipeline combines two leading sequence-based protein-protein interaction predictors, the Protein-protein Interaction Prediction Engine (PIPE), PIPE4, and Scoring PRotein INTeractions (SPRINT) to predict high-confidence interactomes. First, we predicted the top soy interacting protein partners of the Rhg1 and Rhg4 proteins. Both PIPE4 and SPRINT overlap in their predictions with 58 soybean interacting partners, 19 of which had GO terms related to defense. Beginning with the top predicted interactors of Rhg1 and Rhg4, we implement a "guilt by association" in silico proteome-wide approach to identify novel soybean genes that may be involved in SCN resistance. This pipeline identified 1,082 candidate genes whose local interactomes overlap significantly with the Rhg1 and Rhg4 interactomes. Using GO enrichment tools, we highlighted many important genes including five genes with GO terms related to response to the nematode (GO:0009624), namely, Glyma.18G029000, Glyma.11G228300, Glyma.08G120500, Glyma.17G152300, and Glyma.08G265700. This study is the first of its kind to predict interacting partners of known resistance proteins Rhg1 and Rhg4, forming an analysis pipeline that enables researchers to focus their search on high-confidence targets to identify novel SCN resistance genes in soybean.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Eric Arezza
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jeansur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - James Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE 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. 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.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- 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
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- 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
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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Proteomic, Transcriptomic, Mutational, and Functional Assays Reveal the Involvement of Both THF and PLP Sites at the GmSHMT08 in Resistance to Soybean Cyst Nematode. Int J Mol Sci 2022; 23:ijms231911278. [PMID: 36232579 PMCID: PMC9570156 DOI: 10.3390/ijms231911278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
The serine hydroxymethyltransferase (SHMT; E.C. 2.1.2.1) is involved in the interconversion of serine/glycine and tetrahydrofolate (THF)/5,10-methylene THF, playing a key role in one-carbon metabolism, the de novo purine pathway, cellular methylation reactions, redox homeostasis maintenance, and methionine and thymidylate synthesis. GmSHMT08 is the soybean gene underlying soybean cyst nematode (SCN) resistance at the Rhg4 locus. GmSHMT08 protein contains four tetrahydrofolate (THF) cofactor binding sites (L129, L135, F284, N374) and six pyridoxal phosphate (PLP) cofactor binding/catalysis sites (Y59, G106, G107, H134, S190A, H218). In the current study, proteomic analysis of a data set of protein complex immunoprecipitated using GmSHMT08 antibodies under SCN infected soybean roots reveals the presence of enriched pathways that mainly use glycine/serine as a substrate (glyoxylate cycle, redox homeostasis, glycolysis, and heme biosynthesis). Root and leaf transcriptomic analysis of differentially expressed genes under SCN infection supported the proteomic data, pointing directly to the involvement of the interconversion reaction carried out by the serine hydroxymethyltransferase enzyme. Direct site mutagenesis revealed that all mutated THF and PLP sites at the GmSHMT08 resulted in increased SCN resistance. We have shown the involvement of PLP sites in SCN resistance. Specially, the effect of the two Y59 and S190 PLP sites was more drastic than the tested THF sites. This unprecedented finding will help us to identify the biological outcomes of THF and PLP residues at the GmSHMT08 and to understand SCN resistance mechanisms.
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Nissan N, Mimee B, Cober ER, Golshani A, Smith M, Samanfar B. A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode. BIOLOGY 2022; 11:211. [PMID: 35205078 PMCID: PMC8869295 DOI: 10.3390/biology11020211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant-pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Myron Smith
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
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Lakhssassi N, Piya S, Bekal S, Liu S, Zhou Z, Bergounioux C, Miao L, Meksem J, Lakhssassi A, Jones K, Kassem MA, Benhamed M, Bendahmane A, Lambert K, Boualem A, Hewezi T, Meksem K. A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1810-1829. [PMID: 31960590 PMCID: PMC7336373 DOI: 10.1111/pbi.13343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pest affecting soybean production worldwide. SCN resistance requires both the GmSHMT08 and the GmSNAP18 in 'Peking'-type resistance. Here, we describe the molecular interaction between GmSHMT08 and GmSNAP18, which is potentiated by a pathogenesis-related protein GmPR08-Bet VI. Like GmSNAP18 and GmSHMT08, GmPR08-Bet VI expression was induced in response to SCN and its overexpression decreased SCN cysts by 65% in infected transgenic soybean roots. Overexpression of GmPR08-Bet VI did not have an effect on SCN resistance when the two cytokinin-binding sites in GmPR08-Bet VI were mutated, indicating a new role of GmPR08-Bet VI in SCN resistance. GmPR08-Bet VI was mapped to a QTL for resistance to SCN using different mapping populations. GmSHMT08, GmSNAP18 and GmPR08-Bet VI localize to the cytosol and plasma membrane. GmSNAP18 expression and localization hyper-accumulated at the plasma membrane and was specific to the root cells surrounding the nematode in SCN-resistant soybeans. Genes encoding key components of the salicylic acid signalling pathway were induced under SCN infection. GmSNAP18 and GmPR08-Bet VI were also induced under salicylic acid and cytokinin exogenous treatments, while GmSHMT08 was induced only when the resistant GmSNAP18 was present, pointing to the presence of a molecular crosstalk between SCN-resistant genes and defence genes. Expression analysis of GmSHMT08 and GmSNAP18 identified the need of a minimum expression requirement to trigger the SCN resistance reaction. These results provide insight into a new response mechanism towards plant nematode resistance involving haplotype compatibility, gene dosage and hormone signalling.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Catherine Bergounioux
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Long Miao
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | | | - Aicha Lakhssassi
- Faculty of Sciences and TechnologiesUniversity of LorraineNancyFrance
| | - Karen Jones
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Moussa Benhamed
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Abdelhafid Bendahmane
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Kris Lambert
- Department of Crop SciencesUniversity of IllinoisUrbanaILUSA
| | - Adnane Boualem
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
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Chang HX, Wen Z, Tan R, Dong H, Wickland DP, Wang D, Chilvers MI. Linkage Mapping for Foliar Necrosis of Soybean Sudden Death Syndrome. PHYTOPATHOLOGY 2020; 110:907-915. [PMID: 31821112 DOI: 10.1094/phyto-09-19-0330-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sudden death syndrome (SDS) foliar symptoms consist of foliar chlorosis, foliar necrosis, leaf marginal curling, and premature defoliation, but resistance screening has been evaluated mostly based on the overall SDS foliar severity rather than on a specific foliar symptom. This study generated an F2 population derived from crossing the susceptible variety Sloan and the resistant germplasm line PI 243518, which exhibits resistance to both foliar chlorosis and necrosis. A total of 400 F2 lines were evaluated for foliar chlorosis, foliar necrosis, and overall SDS foliar symptoms, separately. Genotyping-by-sequencing was applied to obtain single nucleotide polymorphisms (SNPs) in the F2 population, and linkage mapping using 135 F2 lines with 969 high-quality SNPs identified a locus on chromosome 13 for foliar necrosis and SDS foliar symptoms. The locus partially overlaps with loci previously reported for SDS on chromosome 13, which is the third time the region from 15.98 to 21.00 Mbp has been reproduced independently and therefore qualifies this locus for a new nomenclature proposed as Rfv13-02. In summary, this study generated a new biparental population that enables not only the discovery of a locus for foliar necrosis and SDS foliar symptoms on chromosome 13 but also the potential for advanced exploration of SDS foliar resistance derived from the germplasm line PI 243518.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, U.S.A
| | - Ruijuan Tan
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, U.S.A
| | - Hongxu Dong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, U.S.A
| | - Daniel P Wickland
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, U.S.A
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, U.S.A
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, U.S.A
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Zhang L, Huang W, Peng D, Liu S. Comparative genomic analyses of two segregating mutants reveal seven genes likely involved in resistance to Fusarium equiseti in soybean via whole genome re-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2997-3008. [PMID: 31338526 DOI: 10.1007/s00122-019-03401-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE The candidate genes involved in resistance to Fusarium equiseti in soybean PI 437654 were identified through comparative genomic analyses of mutants via whole genome re-sequencing. The fungus Fusarium infects each stage of the growth and development of soybean and causes soybean (Glycine max (L.)) seed and root rot and seedling damping-off and wilt with a large quantity of annual yield loss worldwide. It is very important to identify the resistant genes in soybean to prevent and control this pathogen. One Fusarium equiseti isolate was previously identified to be incompatible with 'PI 437654' but compatible with a Chinese soybean cultivar 'Zhonghuang 13'. In this study, with the infection of this isolate on the seedling roots of developed PI 437654 mutants, 6 mutants were identified from 500 mutants to significantly alter their phenotypes to F. equiseti compared to wild-type PI 437654. Then, two identified segregating mutants were selected to directly perform whole genome re-sequencing. Finally, through comparative genomic analyses 7 genes including one cluster of 4 nucleotide binding site-leucine-rich repeat genes on one genomic region of chromosome 7, a 60S ribosomal protein L12 gene and 2 uncharacterized genes were identified to be likely involved in the resistance to F. equiseti. These genes will facilitate the breeding of resistant germplasm resources and the identification of resistance of soybean to Fusarium spp.
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Affiliation(s)
- Liuping Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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Swaminathan S, Das A, Assefa T, Knight JM, Da Silva AF, Carvalho JPS, Hartman GL, Huang X, Leandro LF, Cianzio SR, Bhattacharyya MK. Genome wide association study identifies novel single nucleotide polymorphic loci and candidate genes involved in soybean sudden death syndrome resistance. PLoS One 2019; 14:e0212071. [PMID: 30807585 PMCID: PMC6391044 DOI: 10.1371/journal.pone.0212071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 01/17/2023] Open
Abstract
Fusarium virguliforme is a soil borne root pathogen that causes sudden death syndrome (SDS) in soybean [Glycine max (L.) Merrill]. Once the fungus invades the root xylem tissues, the pathogen secretes toxins that cause chlorosis and necrosis in foliar tissues leading to defoliation, flower and pod drop and eventually death of plants. Resistance to F. virguliforme in soybean is partial and governed by over 80 quantitative trait loci (QTL). We have conducted genome-wide association study (GWAS) for a group of 254 plant introductions lines using a panel of approximately 30,000 SNPs and identified 19 single nucleotide polymorphic loci (SNPL) that are associated with 14 genomic regions encoding foliar SDS and eight SNPL associated with seven genomic regions for root rot resistance. Of the identified 27 SNPL, six SNPL for foliar SDS resistance and two SNPL for root rot resistance co-mapped to previously identified QTL for SDS resistance. This study identified 13 SNPL associated with eight novel genomic regions containing foliar SDS resistance genes and six SNPL with five novel regions for root-rot resistance. This study identified five genes carrying nonsynonymous mutations: (i) three of which mapped to previously identified QTL for foliar SDS resistance and (ii) two mapped to two novel regions containing root rot resistance genes. Of the three genes mapped to QTL for foliar SDS resistance genes, two encode LRR-receptors and third one encodes a novel protein with unknown function. Of the two genes governing root rot resistance, Glyma.01g222900.1 encodes a soybean-specific LEA protein and Glyma.10g058700.1 encodes a heparan-alpha-glucosaminide N-acetyltransferase. In the LEA protein, a conserved serine residue was substituted with asparagine; and in the heparan-alpha-glucosaminide N-acetyltransferase, a conserved histidine residue was substituted with an arginine residue. Such changes are expected to alter functions of these two proteins regulated through phosphorylation. The five genes with nonsynonymous mutations could be considered candidate SDS resistance genes and should be suitable molecular markers for breeding SDS resistance in soybean. The study also reports desirable plant introduction lines and novel genomic regions for enhancing SDS resistance in soybean.
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Affiliation(s)
| | - Anindya Das
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
| | - Teshale Assefa
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Joshua M. Knight
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | | | - João P. S. Carvalho
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Glen L. Hartman
- USDA and Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Xiaoqiu Huang
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
| | - Leonor F. Leandro
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Silvia R. Cianzio
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
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