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Soler‐Garzón A, Lopes FS, Roy J, Clevenger J, Myers Z, Korani W, Pereira WA, Song Q, Porch T, McClean PE, Miklas PN. Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations. THE PLANT GENOME 2025; 18:e20538. [PMID: 39653039 PMCID: PMC11726412 DOI: 10.1002/tpg2.20538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 10/18/2024] [Accepted: 11/03/2024] [Indexed: 01/14/2025]
Abstract
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a devastating disease affecting common bean (Phaseolus vulgaris L.) production worldwide. Breeding for resistance to white mold is challenging due to its quantitative inheritance and intricate genetic mechanisms. This research aimed to validate and characterize physiological resistance in the pinto dry bean market class through greenhouse straw tests under controlled conditions and field assessments under natural environments. Classical quantitative trait locus (QTL) mapping and Khufu de novo QTL-seq were employed to detect and narrow QTL intervals and identify candidate genes associated with white mold resistance in two pinto bean recombinant inbred line populations, PT9-5-6/USPT-WM-12 (P2) and PT12-37/VCP-13 (P3). Eleven QTL, five in P2 and six in P3, conditioning white mold resistance were identified. New QTL were discovered including WM1.4 and WM11.5 in P2, and WM1.5 and WM7.7 in P3. Existing major-effect QTL were validated: WM5.4 (34%-phenotypic variation explained) and WM7.4 (20%) in straw tests, and WM2.2 (15%) and WM3.1 (27%) under field conditions. QTL for avoidance traits such as resistance to lodging and late maturity overlapped WM2.2 in P2 and WM1.5, WM3.1, WM5.4, and WM7.7 in P3. WM5.4 (Pv05: 7.0-38.7 Mb) was associated with a large Phaseolus coccineus L. genome introgression in the resistant parent VCP-13. These findings offer narrowed genomic intervals and putative candidate genes for marker-assisted selection targeting white mold resistance improvement in pinto beans.
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Affiliation(s)
- Alvaro Soler‐Garzón
- Irrigated Agriculture Research and Extension CenterWashington State UniversityProsserWashingtonUSA
| | | | - Jayanta Roy
- Department of Plant SciencesNorth Dakota State UniversityFargoNorth DakotaUSA
| | - Josh Clevenger
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Zachary Myers
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Walid Korani
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | | | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA‐ARSBeltsvilleMarylandUSA
| | - Timothy Porch
- USDA‐ARS, Tropical Agricultural Research StationMayagüezPuerto RicoUSA
| | - Phillip E. McClean
- Department of Plant SciencesNorth Dakota State UniversityFargoNorth DakotaUSA
| | - Phillip N. Miklas
- USDA‐ARS, Grain Legume Genetics and Physiology Research UnitProsserWashingtonUSA
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Zhao F, Wang Y, Cheng W, Antwi-Boasiako A, Yan W, Zhang C, Gao X, Kong J, Liu W, Zhao T. Genome-Wide Association Study of Bacterial Blight Resistance in Soybean. PLANT DISEASE 2025; 109:341-351. [PMID: 39254851 DOI: 10.1094/pdis-01-24-0162-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Bacterial blight caused by Pseudomonas syringae pv. glycinea (Psg) is a widespread foliar disease. Although four Resistance to Pseudomonas syringae pv. glycinea (Rpg) 1 to 4 (Rpg1∼4) genes that have been observed to segregate in a Mendelian pattern have been reported to confer resistance to Psg in soybean, the genetic basis of quantitative resistance to bacterial blight in soybean remains unclear. In the present study, the Psg resistance of two soybean association panels consisting of 573 and 213 lines, respectively, was phenotyped in multiple environments in 2014 to 2016. Genome-wide association study was performed using two models, FarmCPU and BLINK, to identify Psg resistance loci. A total of 40 soybean varieties with high level of Psg resistance were identified, and 14 quantitative trait loci (QTLs) were detected on 12 soybean chromosomes. These QTLs were identified for the first time. The majority of the QTLs were detected only in one or the other association panels, while qRPG-18-1 was detected in both association panels for at least one growing season. A total of 46 candidate Psg resistance genes were identified from the qRpg_13_1, qRPG-15-1, and qRPG-18-1 loci based on gene function annotation. In addition, we found the genomic region covering rpg1-b and rpg1-r harbored the synteny with a genomic region on chromosome 15 and identified 16 nucleotide binding site-leucine-rich repeat (NBS-LRR) genes as the candidate Psg resistance genes from the synteny blocks. This study provides new information for dissecting the genetic control of Psg resistance in soybean.
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Affiliation(s)
- Fangzhou Zhao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanan Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Cheng
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Augustine Antwi-Boasiako
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR-CRI), Kumasi AK000-AK911, Fumesua, Ghana
| | - Wenkai Yan
- Bioinformatics Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuewen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiejie Kong
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Yi Y, Luan P, Fan M, Wu X, Sun Z, Shang Z, Yang Y, Li C. Antifungal efficacy of Bacillus amyloliquefaciens ZK-9 against Fusarium graminearum and analysis of the potential mechanism of its lipopeptides. Int J Food Microbiol 2024; 422:110821. [PMID: 38970998 DOI: 10.1016/j.ijfoodmicro.2024.110821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/22/2024] [Accepted: 06/29/2024] [Indexed: 07/08/2024]
Abstract
Fusarium graminearum is a destructive fungal pathogen that seriously threatens wheat production and quality. In the management of fungal infections, biological control is an environmentally friendly and sustainable approach. Here, the antagonistic strain ZK-9 with a broad antifungal activity was identified as Bacillus amyloliquefaciens. ZK-9 could produce extracellular enzymes such as pectinase, protease, cellulase, and amylase, as well as plant growth-promoting substances including IAA and siderophore. Lipopeptides extracted from strain ZK-9 had the high inhibitory effects on the mycelia of F. graminearum with the minimum inhibitory concentration (MIC) of 0.8 mg/mL. Investigation on the action mechanism of lipopeptides showed they could change the morphology of mycelia, damage the cell membrane, lower the content of ergosterol and increase the relative conductivity of membrane, cause nucleic acid and proteins leaking out from the cells, and disrupt the cell membrane permeability. Furthermore, metabolomic analysis of F. graminearum revealed the significant differences in the expression of 100 metabolites between the lipopeptides treatment group and the control group, which were associated with various metabolic pathways, mainly including amino acid biosynthesis, pentose, glucuronate and glycerophospholipid metabolism. In addition, strain ZK-9 inhibited Fusarium crown rot (FCR) with a biocontrol efficacy of 82.14 % and increased the plant height and root length by 24.23 % and 93.25 %, respectively. Moreover, the field control efficacy of strain ZK-9 on Fusarium head blight (FHB) was 71.76 %, and the DON content in wheat grains was significantly reduced by 69.9 %. This study puts valuable insights into the antifungal mechanism of lipopeptides against F. graminearum, and provides a promising biocontrol agent for controlling F. graminearum.
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Affiliation(s)
- Yanjie Yi
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; Food Laboratory of Zhongyuan, Luohe 462300, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China.
| | - Pengyu Luan
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; Food Laboratory of Zhongyuan, Luohe 462300, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Minghao Fan
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Xingquan Wu
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Zhongke Sun
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Zijun Shang
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Yuzhen Yang
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China
| | - Chengwei Li
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; The Key Laboratory of Functional Molecules for Biomedical Research, Zhengzhou 450001, China.
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Wang SY, Zhang YJ, Chen X, Shi XC, Herrera-Balandrano DD, Liu FQ, Laborda P. Biocontrol Methods for the Management of Sclerotinia sclerotiorum in Legumes: A Review. PHYTOPATHOLOGY 2024; 114:1447-1457. [PMID: 38669603 DOI: 10.1094/phyto-01-24-0006-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Sclerotinia sclerotiorum is an economically damaging fungal pathogen that causes Sclerotinia stem rot in legumes, producing enormous yield losses. This pathogen is difficult to control due to its wide host spectrum and ability to produce sclerotia, which are resistant bodies that can remain active for long periods under harsh environmental conditions. Here, the biocontrol methods for the management of S. sclerotiorum in legumes are reviewed. Bacillus strains, which synthesized lipopeptides and volatile organic compounds, showed high efficacies in soybean plants, whereas the highest efficacies for the control of the pathogen in alfalfa and common bean were observed when using Coniothyrium minitans and Streptomyces spp., respectively. The biocontrol efficacies in fields were under 65%, highlighting the lack of strategies to achieve a complete control. Overall, although most studies involved extensive screenings using different biocontrol agent concentrations and application conditions, there is a lack of knowledge regarding the specific antifungal mechanisms, which limits the optimization of the reported methods.
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Affiliation(s)
- Su-Yan Wang
- School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China
| | - Yun-Jiao Zhang
- School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China
| | - Xin Chen
- School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China
| | - Xin-Chi Shi
- School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China
| | | | - Feng-Quan Liu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China
| | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China
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Cheng Y, Lou H, He H, He X, Wang Z, Gao X, Liu J. Genomic and biological control of Sclerotinia sclerotiorum using an extracellular extract from Bacillus velezensis 20507. Front Microbiol 2024; 15:1385067. [PMID: 38596383 PMCID: PMC11002150 DOI: 10.3389/fmicb.2024.1385067] [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: 02/11/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Sclerotinia sclerotiorum is a known pathogen that harms crops and vegetables. Unfortunately, there is a lack of effective biological control measures for this pathogen. Bacillus velezensis 20507 has a strong antagonistic effect on S. Sclerotiorum; however, the biological basis of its antifungal effect is not fully understood. Methods In this study, the broad-spectrum antagonistic microorganisms of B. velezensis 20507 were investigated, and the active antifungal ingredients in this strain were isolated, purified, identified and thermal stability experiments were carried out to explore its antifungal mechanism. Results The B. velezensis 20507 genome comprised one circular chromosome with a length of 4,043,341 bp, including 3,879 genes, 185 tandem repeats, 87 tRNAs, and 27 rRNAs. Comparative genomic analysis revealed that our sequenced strain had the closest genetic relationship with Bacillus velezensis (GenBank ID: NC 009725.2); however, there were significant differences in the positions of genes within the two genomes. It is predicted that B. velezensis 20507 encode 12 secondary metabolites, including difficidin, macrolactin H, fengycin, surfactin, bacillibactin, bacillothiazole A-N, butirosin a/b, and bacillaene. Results showed that B. velezensis 20507 produced various antagonistic effects on six plant pathogen strains: Exserohilum turcicum, Pyricularia oryzae, Fusarium graminearum, Sclerotinia sclerotiorum, Fusarium oxysporum, and Fusarium verticillioides. Acid precipitation followed by 80% methanol leaching is an effective method for isolating the antifungal component ME80 in B. velezensis 20507, which can damage the membranes of S. sclerotiorum hyphae and has good heat resistance. Using high-performance liquid chromatography, and Mass Spectrometry analysis, it is believed that fengycin C72H110N12O20 is the main active antifungal substance. Discussion This study provides new resources for the biological control of S. Sclerotiorum in soybeans and a theoretical basis for further clarification of the mechanism of action of B. velezensis 20507.
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Affiliation(s)
- Yunqing Cheng
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
| | - Hanxiao Lou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
| | - Hongli He
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
| | - Xinyi He
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
| | - Zicheng Wang
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Xin Gao
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
| | - Jianfeng Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin, China
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Zalila-Kolsi I, Ben-Mahmoud A, Al-Barazie R. Bacillus amyloliquefaciens: Harnessing Its Potential for Industrial, Medical, and Agricultural Applications-A Comprehensive Review. Microorganisms 2023; 11:2215. [PMID: 37764059 PMCID: PMC10536829 DOI: 10.3390/microorganisms11092215] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillus amyloliquefaciens, a Gram-positive bacterium, has emerged as a versatile microorganism with significant applications in various fields, including industry, medicine, and agriculture. This comprehensive review aims to provide an in-depth understanding of the characteristics, genetic tools, and metabolic capabilities of B. amyloliquefaciens, while highlighting its potential as a chassis cell for synthetic biology, metabolic engineering, and protein expression. We discuss the bacterium's role in the production of chemicals, enzymes, and other industrial bioproducts, as well as its applications in medicine, such as combating infectious diseases and promoting gut health. In agriculture, B. amyloliquefaciens has demonstrated potential as a biofertilizer, biocontrol agent, and stress tolerance enhancer for various crops. Despite its numerous promising applications, B. amyloliquefaciens remains less studied than its Gram-negative counterpart, Escherichia coli. This review emphasizes the need for further research and development of advanced engineering techniques and genetic editing technologies tailored for B. amyloliquefaciens, ultimately unlocking its full potential in scientific and industrial contexts.
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Affiliation(s)
- Imen Zalila-Kolsi
- Faculty of Medical and Health Sciences, Liwa College, Abu Dhabi P.O. Box 41009, United Arab Emirates;
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar;
| | - Ray Al-Barazie
- Faculty of Medical and Health Sciences, Liwa College, Abu Dhabi P.O. Box 41009, United Arab Emirates;
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