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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. THE NEW PHYTOLOGIST 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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Mulozi L, Vennapusa AR, Elavarthi S, Jacobs OE, Kulkarni KP, Natarajan P, Reddy UK, Melmaiee K. Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple ( Acer saccharum Marshall) saplings. FRONTIERS IN PLANT SCIENCE 2023; 14:1150204. [PMID: 37152134 PMCID: PMC10154611 DOI: 10.3389/fpls.2023.1150204] [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: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of the United States and is economically important for its hardwood and syrup production. Sugar maple trees are highly vulnerable to changing climatic conditions, especially drought, so understanding the physiological, biochemical, and molecular responses is critical. The sugar maple saplings were subjected to drought stress for 7, 14, and 21 days and physiological data collected at 7, 14, and 21 days after stress (DAS) showed significantly reduced chlorophyll and Normalized Difference Vegetation Index with increasing drought stress time. The drought stress-induced biochemical changes revealed a higher accumulation of malondialdehyde, proline, and peroxidase activity in response to drought stress. Transcriptome analysis identified a total of 14,099 differentially expressed genes (DEGs); 328 were common among all stress periods. Among the DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, and ERF), chloroplast-related and stress-responsive genes such as peroxidases, membrane transporters, kinases, and protein detoxifiers were predominant. GO enrichment and KEGG pathway analysis revealed significantly enriched processes related to protein phosphorylation, transmembrane transport, nucleic acids, and metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, and carotenoid biosynthesis in response to drought stress. Time-series transcriptomic analysis revealed changes in gene regulation patterns in eight different clusters, and pathway analysis by individual clusters revealed a hub of stress-responsive pathways. In addition, qRT-PCR validation of selected DEGs revealed that the expression patterns were consistent with transcriptome analysis. The results from this study provide insights into the dynamics of physiological, biochemical, and gene responses to progressive drought stress and reveal the important stress-adaptive mechanisms of sugar maple saplings in response to drought stress.
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Affiliation(s)
- Lungowe Mulozi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Sathya Elavarthi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
| | - Oluwatomi E. Jacobs
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Krishnanand P. Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Purushothaman Natarajan
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Umesh K. Reddy
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
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Inheritance of 2,4-dichlorophenoxyacetic acid (2,4-D) resistance in Amaranthus palmeri. Sci Rep 2022; 12:21822. [PMID: 36528649 PMCID: PMC9759536 DOI: 10.1038/s41598-022-25686-1] [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: 08/10/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
In this study, the inheritance of 2,4-D resistance in a multiple herbicide-resistant Palmer amaranth (KCTR) was investigated. Direct and reciprocal crosses were performed using 2,4-D-resistant KCTR and susceptible KSS plants to generate F1 progenies. 2,4-D dose-response assays were conducted to evaluate the response of progenies from each F1 family along with KCTR and KSS plants in controlled environmental growth chambers. Additionally, 2,4-D-resistant male and female plants from each of the F1 families were used in pairwise crosses to generate pseudo-F2 families. Segregation (resistance or susceptibility) of progenies from the F2 families in response to a discriminatory rate of 2,4-D (i.e., 560 g ae ha-1) was evaluated. Dose-response analysis of F1 progenies derived from direct and reciprocal crosses suggested that the 2,4-D resistance in KCTR is a nuclear trait. Chi-square analyses of F2 segregation data implied that 2,4-D resistance in KCTR is controlled by multiple gene(s). Overall, our data suggest that the 2,4-D resistance in KCTR Palmer amaranth is a nuclear inherited trait controlled by multiple genes. Such resistance can spread both via pollen or seed-mediated gene flow. In future, efforts will be directed towards identifying genes mediating 2,4-D resistance in KCTR population.
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Xu Y, Li S, Hao L, Li X, Zheng M. Tribenuron-methyl-resistant Descurainia sophia L. exhibits negative cross-resistance to imazethapyr conferred by a Pro197Ser mutation in acetolactate synthase and reduced metabolism. PEST MANAGEMENT SCIENCE 2022; 78:1467-1473. [PMID: 34951107 DOI: 10.1002/ps.6764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Descurainia sophia L. is one of the most notorious weeds infesting winter wheat in China. Mutations at Pro197 in acetolactate synthase (ALS) results in resistance of D. sophia to tribenuron-methyl and cross-resistance to many ALS inhibitors. Negative cross-resistance to imazethapyr was observed in tribenuron-methyl-resistant (TR) D. sophia with the Pro197Ser mutation in a previous study. In the present research, another TR D. sophia with the Pro197Ser mutation was obtained. To explore the mechanisms of negative cross-resistance, the ALS sensitivity, the absorption and metabolism of imazethapyr in tribenuron-methyl-susceptible (TS) and TR D. sophia were studied. RESULTS The TR D. sophia population with the Pro197Ser mutation (pHB23) displayed negative cross-resistance to imazethapyr and no cross-resistance to imazamox and imazapic. In contrast, TR D. sophia populations with other Pro197 mutations had no or low resistance to imazethapyr. The ALS in the pHB23 population was more susceptible to imazethapyr than that in the TS population. There was no difference in the absorption of imazethapyr, imazamox, and imazapic between TS and pHB23 plants. However, the metabolism of imazethapyr in TS D. sophia was faster than that in pHB23 plants up to 1 week after treatment. There was no significant difference in the metabolism of imazamox and imazapic between TS and pHB23 plants. CONCLUSION The TR D. sophia population with the Pro197Ser mutation exhibited negative cross-resistance to imazethapyr, which was likely due to reduced metabolism and increased sensitivity of ALS to imazethapyr. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Yufang Xu
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Shuang Li
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Lubo Hao
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Li
- College of Science, China Agricultural University, Beijing, 100193, China
| | - Mingqi Zheng
- College of Science, China Agricultural University, Beijing, 100193, China
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Pandian BA, Sexton-Bowser S, Prasad PV, Jugulam M. Current status and prospects of herbicide-resistant grain sorghum (Sorghum bicolor). PEST MANAGEMENT SCIENCE 2022; 78:409-415. [PMID: 34532972 DOI: 10.1002/ps.6644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Grain sorghum is a versatile crop, which can thrive under limited water and other inputs. However, crop loss from weed infestation continues to be a major constraint in grain sorghum production. Particularly, post-emergence grass weed control is a great challenge in grain sorghum due to the lack of herbicide options. Unlike in other major crops, such as maize or soybean, herbicide-resistant sorghum technology that can facilitate weed control throughout crop growing season is not available to growers yet. The development of herbicide-resistant sorghum can have potential to improve weed management, including post-emergence grass weed control. One of the major concerns in the development of such technology in sorghum is escape of resistance traits into weedy relatives of sorghum (e.g. shattercane and johnsongrass). This review focuses on sources of herbicide resistance in sorghum, the status of the development of herbicide-resistant sorghum technologies, overview of breeding methods, and limitations in the development of such sorghum technology as well as economic benefits for sorghum growers. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Balaji A Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Pv Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
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Chen J, Hu H, Ye K, Wang W, Xu D. Synthesis of Novel Pyrimidinylselenium Compounds as Acetolactate Synthase‐Inhibiting Herbicides. ChemistrySelect 2022. [DOI: 10.1002/slct.202103763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jinglei Chen
- School of Pharmacy Changzhou University Changzhou 213164 P. R. China
| | - Hang Hu
- School of Pharmacy Changzhou University Changzhou 213164 P. R. China
| | - Kai Ye
- School of Pharmacy Changzhou University Changzhou 213164 P. R. China
| | - Wei Wang
- FRD Science & Technology Jiangshu) Co., Ltd P. R. China
| | - Defeng Xu
- School of Pharmacy Changzhou University Changzhou 213164 P. R. China
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