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Einspanier S, Tominello-Ramirez C, Hasler M, Barbacci A, Raffaele S, Stam R. High-Resolution Disease Phenotyping Reveals Distinct Resistance Mechanisms of Tomato Crop Wild Relatives against Sclerotinia sclerotiorum. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0214. [PMID: 39105186 PMCID: PMC11298253 DOI: 10.34133/plantphenomics.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 08/07/2024]
Abstract
Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR's genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host's genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.
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Affiliation(s)
- Severin Einspanier
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
| | - Christopher Tominello-Ramirez
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
| | - Mario Hasler
- Lehrfach Variationsstatistik, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, Kiel, 24118 Kiel, Germany
| | - Adelin Barbacci
- Laboratoire des Interactions Plantes Microorganismes Environnement (LIPME), INRAE, CNRS, Castanet Tolosan Cedex, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Microorganismes Environnement (LIPME), INRAE, CNRS, Castanet Tolosan Cedex, France
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
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Hohenfeld CS, de Oliveira SAS, Ferreira CF, Mello VH, Margarido GRA, Passos AR, de Oliveira EJ. Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance. Sci Rep 2024; 14:10587. [PMID: 38719851 PMCID: PMC11078935 DOI: 10.1038/s41598-024-60847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.
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Affiliation(s)
- Camila Santiago Hohenfeld
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | | | - Claudia Fortes Ferreira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil
| | - Victor Hugo Mello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Adriana Rodrigues Passos
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil.
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Liu G, Fang Y, Liu X, Jiang J, Ding G, Wang Y, Zhao X, Xu X, Liu M, Wang Y, Yang C. Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1369650. [PMID: 38628361 PMCID: PMC11019568 DOI: 10.3389/fpls.2024.1369650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Powdery mildew disease (PMD) is caused by the obligate biotrophic fungus Microsphaera diffusa Cooke & Peck (M. diffusa) and results in significant yield losses in soybean (Glycine max (L.) Merr.) crops. By identifying disease-resistant genes and breeding soybean accessions with enhanced resistance, we can effectively mitigate the detrimental impact of PMD on soybeans. We analyzed PMD resistance in a diversity panel of 315 soybean accessions in two locations over 3 years, and candidate genes associated with PMD resistance were identified through genome-wide association studies (GWAS), haplotype analysis, qRT-PCR, and EMS mutant analysis. Based on the GWAS approach, we identified a region on chromosome 16 (Chr16) in which 21 genes form a gene cluster that is highly correlated with PMD resistance. In order to validate and refine these findings, we conducted haplotype analysis of 21 candidate genes and indicated there are single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) variations of Glyma.16G214000, Glyma.16G214200, Glyma.16G215100 and Glyma.16G215300 within the coding and promoter regions that exhibit a strong association with resistance against PMD. Subsequent structural analysis of candidate genes within this cluster revealed that in 315 accessions, the majority of accessions exhibited resistance to PMD when Glyma.16G214300, Glyma.16G214800 and Glyma.16G215000 were complete; however, they demonstrated susceptibility to PMD when these genes were incomplete. Quantitative real-time PCR assays (qRT-PCR) of possible candidate genes showed that 14 candidate genes (Glyma.16G213700, Glyma.16G213800, Glyma.16G213900, Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214500, Glyma.16G214585, Glyma.16G214669, Glyma.16G214700, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300) were involved in PMD resistance. Finally, we evaluated the PMD resistance of mutant lines from the Williams 82 EMS mutations library, which revealed that mutants of Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300, exhibited sensitivity to PMD. Combined with the analysis results of GWAS, haplotypes, qRT-PCR and mutants, the genes Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300 were identified as highly correlated with PMD resistance. The candidate genes identified above are all NLR family genes, and these discoveries deepen our understanding of the molecular basis of PMD resistance in soybeans and will be useful for guiding breeding strategies.
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Affiliation(s)
- Guoqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Yuan Fang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xueling Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Jiacan Jiang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Guangquan Ding
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Yongzhen Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Xueqian Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Xiaomin Xu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Mengshi Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Yingxiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Cunyi Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
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Kohli M, Bansal H, Mishra GP, Dikshit HK, Reddappa SB, Roy A, Sinha SK, Shivaprasad K, Kumari N, Kumar A, Kumar RR, Nair RM, Aski M. Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean ( Vigna radiata L. Wilczek) using genotyping by sequencing approach. PeerJ 2024; 12:e16653. [PMID: 38288464 PMCID: PMC10823994 DOI: 10.7717/peerj.16653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.
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Affiliation(s)
- Manju Kohli
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | | | - Anirban Roy
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Subodh Kumar Sinha
- Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India
| | - K.M. Shivaprasad
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Nikki Kumari
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Ranjeet R. Kumar
- Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | | | - Muraleedhar Aski
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
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Sang Y, Liu X, Yuan C, Yao T, Li Y, Wang D, Zhao H, Wang Y. Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China. BMC PLANT BIOLOGY 2023; 23:625. [PMID: 38062401 PMCID: PMC10702129 DOI: 10.1186/s12870-023-04646-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure. RESULTS The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance. CONCLUSIONS The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.
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Affiliation(s)
- Yongsheng Sang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, 130118, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Tong Yao
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824, USA
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
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de Ronne M, Légaré G, Belzile F, Boyle B, Torkamaneh D. 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes. PLANT METHODS 2023; 19:13. [PMID: 36740716 PMCID: PMC9899395 DOI: 10.1186/s13007-023-00990-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a "standard" ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500-1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada
| | - Gaétan Légaré
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada.
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada.
- Institut intelligence et données (IID), Université Laval, Quebec, 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: 26] [Impact Index Per Article: 13.0] [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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8
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Derbyshire MC, Newman TE, Khentry Y, Owolabi Taiwo A. The evolutionary and molecular features of the broad-host-range plant pathogen Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2022; 23:1075-1090. [PMID: 35411696 PMCID: PMC9276942 DOI: 10.1111/mpp.13221] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/09/2022] [Accepted: 03/25/2022] [Indexed: 05/21/2023]
Abstract
Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of plant species, including many of the world's most important crops. Key features of S. sclerotiorum include its extraordinary host range, preference for dicotyledonous plants, relatively slow evolution, and production of protein effectors that are active in multiple host species. Plant resistance to this pathogen is highly complex, typically involving numerous polymorphisms with infinitesimally small effects, which makes resistance breeding a major challenge. Due to its economic significance, S. sclerotiorum has been subjected to a large amount of molecular and evolutionary research. In this updated pathogen profile, we review the evolutionary and molecular features of S. sclerotiorum and discuss avenues for future research into this important species.
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Affiliation(s)
- Mark C. Derbyshire
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Toby E. Newman
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Yuphin Khentry
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Akeem Owolabi Taiwo
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
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9
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Molecular Breeding to Overcome Biotic Stresses in Soybean: Update. PLANTS 2022; 11:plants11151967. [PMID: 35956444 PMCID: PMC9370206 DOI: 10.3390/plants11151967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important leguminous crop and biotic stresses are a global concern for soybean growers. In recent decades, significant development has been carried outtowards identification of the diseases caused by pathogens, sources of resistance and determination of loci conferring resistance to different diseases on linkage maps of soybean. Host-plant resistance is generally accepted as the bestsolution because of its role in the management of environmental and economic conditions of farmers owing to low input in terms of chemicals. The main objectives of soybean crop improvement are based on the identification of sources of resistance or tolerance against various biotic as well as abiotic stresses and utilization of these sources for further hybridization and transgenic processes for development of new cultivars for stress management. The focus of the present review is to summarize genetic aspects of various diseases caused by pathogens in soybean and molecular breeding research work conducted to date.
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10
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Sun M, Na C, Jing Y, Cui Z, Li N, Zhan Y, Teng W, Li Y, Li W, Zhao X, Han Y. Genome-Wide Association Analysis and Gene Mining of Resistance to China Race 1 of Frogeye Leaf Spot in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867713. [PMID: 35812941 PMCID: PMC9257224 DOI: 10.3389/fpls.2022.867713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Soybean frogeye leaf spot (FLS) is a worldwide fungal disease. Its higher occurrence frequency and wider distribution range always led to severe yield losses of soybean, therefore, breeding new cultivars with FLS resistance has been an important breeding goal for soybean breeders. In this study, an association panel of 183 representative soybean accessions was used to evaluate their resistance to FLS race 1, and to identify quantitative trait nucleotides (QTNs) and candidate genes based on genome-wide association study (GWAS) and high-throughput single-nucleotide polymorphisms (SNPs). A total of 23,156 high-quality SNPs were developed using the specific locus-amplified fragment sequencing (SLAF-seq) approach. Finally, 13 novel association signals associated with FLS race 1 resistance were identified by the compressed mixed linear model (CMLM). In addition, 119 candidate genes were found within the 200-kb flanking genomic region of these 13 peak SNPs. Based on the gene-based association analysis, haplotype analysis, expression pattern analysis, and virus-induced gene silencing (VIGS) systems, four genes (Glyma.05G121100, Glyma.17G228300, Glyma.19G006900, and Glyma.19G008700) were preliminarily proved to play an important role in the soybean resistance to FLS race 1.
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Affiliation(s)
- Maolin Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Chen Na
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yan Jing
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhihui Cui
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Na Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
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11
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Belzile F, Jean M, Torkamaneh D, Tardivel A, Lemay MA, Boudhrioua C, Arsenault-Labrecque G, Dussault-Benoit C, Lebreton A, de Ronne M, Tremblay V, Labbé C, O’Donoughue L, St-Amour VTB, Copley T, Fortier E, Ste-Croix DT, Mimee B, Cober E, Rajcan I, Warkentin T, Gagnon É, Legay S, Auclair J, Bélanger R. The SoyaGen Project: Putting Genomics to Work for Soybean Breeders. FRONTIERS IN PLANT SCIENCE 2022; 13:887553. [PMID: 35557742 PMCID: PMC9087807 DOI: 10.3389/fpls.2022.887553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.
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Affiliation(s)
- François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Martine Jean
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Aurélie Tardivel
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Marc-André Lemay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Chiheb Boudhrioua
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | | | | | - Amandine Lebreton
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Vanessa Tremblay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Caroline Labbé
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Louise O’Donoughue
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Vincent-Thomas Boucher St-Amour
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Tanya Copley
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Eric Fortier
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Tom Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Éric Gagnon
- Semences Prograin Inc., Saint-Césaire, QC, Canada
- Sevita Genetics, Inkerman, ON, Canada
| | | | | | - Richard Bélanger
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
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12
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Ferreira EGC, Marcelino-Guimarães FC. Mapping Major Disease Resistance Genes in Soybean by Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:313-340. [PMID: 35641772 DOI: 10.1007/978-1-0716-2237-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most valuable agricultural crops in the world. Besides, this legume is constantly attacked by a wide range of pathogens (fungi, bacteria, viruses, and nematodes) compromising yield and increasing production costs. One of the major disease management strategies is the genetic resistance provided by single genes and quantitative trait loci (QTL). Identifying the genomic regions underlying the resistance against these pathogens on soybean is one of the first steps performed by molecular breeders. In the past, genetic mapping studies have been widely used to discover these genomic regions. However, over the last decade, advances in next-generation sequencing technologies and their subsequent cost decreasing led to the development of cost-effective approaches to high-throughput genotyping. Thus, genome-wide association studies applying thousands of SNPs in large sets composed of diverse soybean accessions have been successfully done. In this chapter, a comprehensive review of the majority of GWAS for soybean diseases published since this approach was developed is provided. Important diseases caused by Heterodera glycines, Phytophthora sojae, and Sclerotinia sclerotiorum have been the focus of the several GWAS. However, other bacterial and fungi diseases also have been targets of GWAS. As such, this GWAS summary can serve as a guide for future studies of these diseases. The protocol begins by describing several considerations about the pathogens and bringing different procedures of molecular characterization of them. Advice to choose the best isolate/race to maximize the discovery of multiple R genes or to directly map an effective R gene is provided. A summary of protocols, methods, and tools to phenotyping the soybean panel is given to several diseases. We also give details of options of DNA extraction protocols and genotyping methods, and we describe parameters of SNP quality to soybean data. Websites and their online tools to obtain genotypic and phenotypic data for thousands of soybean accessions are highlighted. Finally, we report several tricks and tips in Subheading 4, especially related to composing the soybean panel as well as generating and analyzing the phenotype data. We hope this protocol will be helpful to achieve GWAS success in identifying resistance genes on soybean.
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13
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Rana K, Ding Y, Banga SS, Liao H, Zhao S, Yu Y, Qian W. Sclerotinia sclerotiorum Thioredoxin1 (SsTrx1) is required for pathogenicity and oxidative stress tolerance. MOLECULAR PLANT PATHOLOGY 2021; 22:1413-1426. [PMID: 34459563 PMCID: PMC8518572 DOI: 10.1111/mpp.13127] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
Sclerotinia sclerotiorum infects host plant tissues by inducing necrosis to source nutrients needed for its establishment. Tissue necrosis results from an enhanced generation of reactive oxygen species (ROS) at the site of infection and apoptosis. Pathogens have evolved ROS scavenging mechanisms to withstand host-induced oxidative damage. However, the genes associated with ROS scavenging pathways are yet to be fully investigated in S. sclerotiorum. We selected the S. sclerotiorum Thioredoxin1 gene (SsTrx1) for our investigations as its expression is significantly induced during S. sclerotiorum infection. RNA interference-induced silencing of SsTrx1 in S. sclerotiorum affected the hyphal growth rate, mycelial morphology, and sclerotial development under in vitro conditions. These outcomes confirmed the involvement of SsTrx1 in promoting pathogenicity and oxidative stress tolerance of S. sclerotiorum. We next constructed an SsTrx1-based host-induced gene silencing (HIGS) vector and mobilized it into Arabidopsis thaliana (HIGS-A) and Nicotiana benthamiana (HIGS-N). The disease resistance analysis revealed significantly reduced pathogenicity and disease progression in the transformed genotypes as compared to the nontransformed and empty vector controls. The relative gene expression of SsTrx1 increased under oxidative stress. Taken together, our results show that normal expression of SsTrx1 is crucial for pathogenicity and oxidative stress tolerance of S. sclerotiorum.
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Affiliation(s)
- Kusum Rana
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Yijuan Ding
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Surinder S. Banga
- Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
| | - Hongmei Liao
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Siqi Zhao
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Yang Yu
- College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Wei Qian
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
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14
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Mwape VW, Khentry Y, Newman TE, Denton-Giles M, Derbyshire MC, Chen K, Berger J, Kamphuis LG. Identification of Sources of Sclerotinia sclerotiorum Resistance in a Collection of Wild Cicer Germplasm. PLANT DISEASE 2021; 105:2314-2324. [PMID: 33851865 DOI: 10.1094/pdis-02-21-0367-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sclerotinia sclerotiorum is an important fungal pathogen of chickpea (Cicer arietinum L.), and it can cause yield losses up to 100%. The wild progenitors are much more diverse than domesticated chickpea, and this study describes how this relates to S. sclerotiorum resistance. Initially, the pathogenicity of nine Australian S. sclerotiorum isolates was examined on three Cicer lines to develop a robust phenotyping assay, and significant differences in isolate aggressiveness were identified with six isolates being classed as highly aggressive and three as moderately aggressive. We identified two S. sclerotiorum isolates, CU8.20 and CU10.12, to be highly aggressive and moderately aggressive, respectively. A subsequent phenotyping assay was conducted using the two isolates to evaluate 86 wild Cicer accessions (Cicer reticulatum and Cicer echinospermum) and two C. arietinum varieties for resistance to S. sclerotiorum. A subset of 12 genotypes was further evaluated, and subsequently, two wild Cicer accessions with consistently high levels of resistance to S. sclerotiorum were examined using the initially characterized nine isolates. Wild Cicer accessions Karab_084 and Deste_063 demonstrated consistent partial resistance to S. sclerotiorum. There were significant differences in responses to S. sclerotiorum across wild Cicer collection sites. The Cermik, Karabahce, and Destek sites' responses to the aggressive isolate CU8.20 ranged from resistant to susceptible, highlighting an interaction between isolate genotype and chickpea collection site for sclerotinia stem rot resistance. This is the first evidence of partial stem resistance identified in wild Cicer germplasm, which can be adopted in chickpea breeding programs to enhance S. sclerotiorum resistance in future chickpea varieties.
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Affiliation(s)
- Virginia W Mwape
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Kefei Chen
- Statistics for the Australian Grains Industry-West, Curtin University, Bentley, WA 6102, Australia
| | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
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15
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Torkamaneh D, Laroche J, Boyle B, Hyten DL, Belzile F. A bumper crop of SNPs in soybean through high-density genotyping-by-sequencing (HD-GBS). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:860-862. [PMID: 33476468 PMCID: PMC8131051 DOI: 10.1111/pbi.13551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/14/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Davoud Torkamaneh
- Département de PhytologieUniversité LavalQuébec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
- Department of Plant AgricultureUniversity of GuelphGuelphONCanada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
| | - David L. Hyten
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - François Belzile
- Département de PhytologieUniversité LavalQuébec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
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16
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Alekcevetch JC, de Lima Passianotto AL, Ferreira EGC, Dos Santos AB, da Silva DCG, Dias WP, Belzile F, Abdelnoor RV, Marcelino-Guimarães FC. Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:777-792. [PMID: 33469696 DOI: 10.1007/s00122-020-03723-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/03/2020] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE A locus on chromosome 13, containing multiple TIR-NB-LRR genes and SNPs associated with M. javanica resistance, was identified using a combination of GWAS, resequencing, genetic mapping and expression profiling. Meloidogyne javanica, a root-knot nematode, is an important problem in soybean-growing areas, leading to severe yield losses. Some accessions have been identified carrying resistance loci to this nematode. In this study, a set of 317 soybean accessions was characterized for resistance to M. javanica. A genome-wide association study was performed using SNPs from genotyping-by-sequencing, and a region of 29.2 kb on chromosome 13 was identified. An analysis of haplotypes showed that SNPs were able to discriminate between susceptible and resistant accessions, with 25 accessions sharing the haplotype associated with resistance. Furthermore, five accessions that exhibited resistance without carrying this haplotype may carry different loci conferring resistance to M. javanica. We also conducted the screening of the SNPs in the USDA soybean germplasm, revealing that several soybean accessions previously reported as resistant to other nematodes also shared the resistance haplotype on chromosome 13. Two SNP-based TaqMan® assays were developed and validated in two panels of soybean cultivars and in biparental populations. In silico analysis of the region associated with resistance identified the occurrence of genes with structural similarity with classical major resistance genes (NBS-LRR genes). Specifically, several nonsynonymous SNPs were observed in Glyma.13g194800 and Glyma.13g194900. The expression profile of these candidate genes demonstrated that the two gene models were up-regulated in the resistance source PI 505,099 after nematode infection. Overall, the SNPs associated with resistance and the genes identified constitute an important tool for introgression of resistance to the root-knot nematode by marker-assisted selection in soybean breeding programs.
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Affiliation(s)
| | | | | | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - Danielle Cristina Gregório da Silva
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - Waldir Pereira Dias
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
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