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Alam O, Purugganan MD. Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. THE PLANT CELL 2024; 36:1227-1241. [PMID: 38243576 PMCID: PMC11062453 DOI: 10.1093/plcell/koae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, 10028, USA
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Ramírez Martínez J, Guillou S, Le Prieur S, Di Vittorio P, Bonal F, Taliadoros D, Gueret E, Fournier E, Stukenbrock EH, Valade R, Gladieux P. Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen. Microb Genom 2024; 10:001241. [PMID: 38713188 PMCID: PMC11170133 DOI: 10.1099/mgen.0.001241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
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Affiliation(s)
- Julie Ramírez Martínez
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | - Pauline Di Vittorio
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florelle Bonal
- UMR AGAP (Amélioration génétique et adaptation des plantes), Montpellier, France
| | - Demetris Taliadoros
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Eva H. Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | | | - Pierre Gladieux
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Ahmad MF, Ahmad FA, Alsayegh AA, Zeyaullah M, AlShahrani AM, Muzammil K, Saati AA, Wahab S, Elbendary EY, Kambal N, Abdelrahman MH, Hussain S. Pesticides impacts on human health and the environment with their mechanisms of action and possible countermeasures. Heliyon 2024; 10:e29128. [PMID: 38623208 PMCID: PMC11016626 DOI: 10.1016/j.heliyon.2024.e29128] [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: 08/31/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Pesticides are chemical constituents used to prevent or control pests, including insects, rodents, fungi, weeds, and other unwanted organisms. Despite their advantages in crop production and disease management, the use of pesticides poses significant hazards to the environment and public health. Pesticide elements have now perpetually entered our atmosphere and subsequently contaminated water, food, and soil, leading to health threats ranging from acute to chronic toxicities. Pesticides can cause acute toxicity if a high dose is inhaled, ingested, or comes into contact with the skin or eyes, while prolonged or recurrent exposure to pesticides leads to chronic toxicity. Pesticides produce different types of toxicity, for instance, neurotoxicity, mutagenicity, carcinogenicity, teratogenicity, and endocrine disruption. The toxicity of a pesticide formulation may depend on the specific active ingredient and the presence of synergistic or inert compounds that can enhance or modify its toxicity. Safety concerns are the need of the hour to control contemporary pesticide-induced health hazards. The effectiveness and implementation of the current legislature in providing ample protection for human health and the environment are key concerns. This review explored a comprehensive summary of pesticides regarding their updated impacts on human health and advanced safety concerns with legislation. Implementing regulations, proper training, and education can help mitigate the negative impacts of pesticide use and promote safer and more sustainable agricultural practices.
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Affiliation(s)
- Md Faruque Ahmad
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Fakhruddin Ali Ahmad
- Department of Basic and Applied Science, School of Engineering and Science, G.D Goenka University, Gururgram, Haryana, 122103, India
| | - Abdulrahman A. Alsayegh
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Md. Zeyaullah
- Department of Basic Medical Science, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha, Saudi Arabia
| | - Abdullah M. AlShahrani
- Department of Basic Medical Science, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha, Saudi Arabia
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha, Saudi Arabia
| | - Abdullah Ali Saati
- Department of Community Medicine & Pilgrims Healthcare, Faculty of Medicine, Umm Al-Qura University, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Ehab Y. Elbendary
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Nahla Kambal
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohamed H. Abdelrahman
- College of Applied Medical Sciences, Medical Laboratory Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Sohail Hussain
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jazan, 45142, Saudi Arabia
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Segbefia W, Singh V, Fuller MG, Yue Z, de Souza FR, Tseng TM. Assessment of Allelopathic Potential of Cotton Chromosome Substitution Lines. PLANTS (BASEL, SWITZERLAND) 2024; 13:1102. [PMID: 38674510 PMCID: PMC11054950 DOI: 10.3390/plants13081102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Weed interference consistently poses a significant agronomic challenge in cotton production, leading to unfavorable direct and indirect consequences. Consequently, the predominant strategy employed to manage weeds is the application of synthetic herbicides. However, this extensive reliance has resulted in the development of herbicide-resistant weed populations due to the prolonged use of a single herbicide and the lack of rotation. This project focused on identifying weed-suppressive cotton chromosome substitution (CS) lines. These CS lines closely resemble the parent TM-1, an upland cotton derivative (Gossypium hirsutum). Each CS line carries a single chromosome or chromosome arm exchanged from G. barbadense, G. tomentosum, or G. mustelinum within the TM-1 background. In a greenhouse experiment utilizing a stepwise approach, five CS lines, along with two conventional varieties (Enlist and UA48) and the parent line (TM1), were assessed to determine their potential for suppressing Palmer amaranth growth. The plant height was measured 7, 14, and 21 days after establishment, and the chlorophyll content was measured 21 days after establishment. The results revealed varying levels of chlorophyll reduction in Palmer amaranth, with the Enlist variety displaying the lowest reduction (32%) and TM-1 exhibiting the highest (78%). Within 14 days of establishment, the CS lines T26lo, BNTN 1-15, and T11sh demonstrated substantial suppression of Palmer amaranth height, with reductions of 79, 70, and 71%, respectively. Conversely, Enlist displayed the least effective performance among the CS lines. Moreover, CS22, CS49, CS50, CS34, UA48, and CS23 displayed a decreasing trend in reducing Palmer amaranth height from 14 to 21 days after establishment. This research demonstrates the inherent herbicidal attributes within cotton CS lines against Palmer amaranth. In light of the versatile applications of cotton fibers and the unique characteristics of the G. hirsutum genome, this study investigates the potential of specific cotton lines in enhancing weed management practices. By elucidating the implications of our findings, we aim to contribute to promoting sustainability and developing alternatives to synthetic herbicides in agricultural systems.
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Affiliation(s)
| | | | | | | | | | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (W.S.); (V.S.); (M.G.F.); (Z.Y.); (F.R.d.S.)
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5
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Wei S, Liu L, Chen G, Yang H, Huang L, Gong G, Luo P, Zhang M. Molecular evolution and phylogeographic analysis of wheat dwarf virus. Front Microbiol 2024; 15:1314526. [PMID: 38419641 PMCID: PMC10901289 DOI: 10.3389/fmicb.2024.1314526] [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: 10/10/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10-4 substitutions/site/year (95% credibility interval, 2.828 × 10-4-5.723 × 10-4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517-1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Linwen Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Liang Huang
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - PeiGao Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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El-Nagar MMF, Elsisi AE. Exposure to bromoxynil octanoate herbicide induces oxidative stress, inflammation, and apoptosis in testicular tissue via modulating NF-кB pathway. Food Chem Toxicol 2023; 180:114008. [PMID: 37660944 DOI: 10.1016/j.fct.2023.114008] [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: 07/17/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Bromoxynil octanoate (BO) is a herbicide necessary for plant growth and production. However, it may cause damage to environment and humans. This study aimed to investigate the potential testicular toxicity of BO and its possible underlying mechanisms. Male Albino (Sprague Dawley) rats were administered BO in different doses (5, 10, 20, and 40 mg/kg/BW; P.O.) daily for 21 days. Testicular function was evaluated by determining count and viability of epididymal sperm, and testosterone. In addition, the following parameters were assessed; MDA, NO, and H2O2 as oxidative stress markers; SOD, CAT, GPx, GST, and GSH as antioxidant markers; NF-ĸB-P65 and IL-18 as inflammatory markers; caspase-9 and caspase-3 as apoptotic markers; gene expression of NF-ĸB-P65, TNF-α, BAX, Bcl-2, and caspase-3; and histopathological examination of epididymis and testis sections. The results showed a significant (P < 0.05) increase in MDA, NO, H2O2, IL-18, and caspase-9 content, NF-ĸB-P65, TNF-α, Bax, and Caspase-3 expression as compared to control. Furthermore, the count and viability of epididymal sperm, testosterone level, SOD, CAT, GPx, GST, and GSH content, and Bcl-2 expression showed a significant (P < 0.05) decrease as compared to control. In conclusion BO-induced testicular damage by altering oxidation, inflammation, and apoptosis.
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Affiliation(s)
- Maysa M F El-Nagar
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Alaa E Elsisi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt.
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Razzaq MK, Hina A, Abbasi A, Karikari B, Ashraf HJ, Mohiuddin M, Maqsood S, Maqsood A, Haq IU, Xing G, Raza G, Bhat JA. Molecular and genetic insights into secondary metabolic regulation underlying insect-pest resistance in legumes. Funct Integr Genomics 2023; 23:217. [PMID: 37392308 DOI: 10.1007/s10142-023-01141-w] [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: 12/27/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/03/2023]
Abstract
Insect pests pose a major threat to agricultural production, resulting in significant economic losses for countries. A high infestation of insects in any given area can severely reduce crop yield and quality. This review examines the existing resources for managing insect pests and highlights alternative eco-friendly techniques to enhance insect pest resistance in legumes. Recently, the application of plant secondary metabolites has gained popularity in controlling insect attacks. Plant secondary metabolites encompass a wide range of compounds such as alkaloids, flavonoids, and terpenoids, which are often synthesized through intricate biosynthetic pathways. Classical methods of metabolic engineering involve manipulating key enzymes and regulatory genes to enhance or redirect the production of secondary metabolites in plants. Additionally, the role of genetic approaches, such as quantitative trait loci mapping, genome-wide association (GWAS) mapping, and metabolome-based GWAS in insect pest management is discussed, also, the role of precision breeding, such as genome editing technologies and RNA interference for identifying pest resistance and manipulating the genome to develop insect-resistant cultivars are explored, highlighting the positive contribution of plant secondary metabolites engineering-based resistance against insect pests. It is suggested that by understanding the genes responsible for beneficial metabolite compositions, future research might hold immense potential to shed more light on the molecular regulation of secondary metabolite biosynthesis, leading to advancements in insect-resistant traits in crop plants. In the future, the utilization of metabolic engineering and biotechnological methods may serve as an alternative means of producing biologically active, economically valuable, and medically significant compounds found in plant secondary metabolites, thereby addressing the challenge of limited availability.
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Affiliation(s)
- Muhammad Khuram Razzaq
- Soybean Research Institute & MARA National Centre for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Aiman Hina
- Ministry of Agriculture (MOA) National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Murree, 47150, Pakistan
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Hafiza Javaria Ashraf
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Mohiuddin
- Environmental Management Consultants (EMC) Private Limited, Islamabad, 44000, Pakistan
| | - Sumaira Maqsood
- Department of Environmental Sciences, Kohsar University Murree, Murree, 47150, Pakistan
| | - Aqsa Maqsood
- Department of Zoology, University of Central Punjab, Bahawalpur, 63100, Pakistan
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Guangnan Xing
- Soybean Research Institute & MARA National Centre for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering Faisalabad, Faisalabad, Pakistan
| | - Javaid Akhter Bhat
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China
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Wei S, Chen G, Yang H, Huang L, Gong G, Luo P, Zhang M. Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes. Virol J 2023; 20:130. [PMID: 37340422 DOI: 10.1186/s12985-023-02084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10- 4 (4.700 × 10- 4-1.228 × 10- 3) and 8.671 × 10- 4 (6.143 × 10- 4-1.130 × 10- 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040-1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang Huang
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - PeiGao Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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Tikoria R, Kaur A, Ohri P. Physiological, biochemical and structural changes in tomato plants by vermicompost application in different exposure periods under glass house conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107656. [PMID: 37001305 DOI: 10.1016/j.plaphy.2023.107656] [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: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
In modern era, various inorganic fertilizers and pesticides are used as plant growth supplements in a variety of crop in order to gain maximum output and also reported as hazardous to mankind as well as environment. In addition, some of the plants died in initial phase of the growth after germination due to poor nutrient content of the soil or exposure to biotic stresses. In the beginning of sustainable agriculture, these chemical fertilizers were replaced with some alternative growth boosters such as organic fertilizers. In the present study, vermicompost was prepared using garden waste and cattle dung followed by analysis of various physico-chemical properties. Then tomato seeds were allowed to germinate in soil and supplemented with different doses of vermicompost (0-100%). The plants were harvested after 10 and 45 days of their germination and tissues were subjected to analysis of various morphological and biochemical parameters. Morphological parameters included root length, shoot length, root fresh weight, shoot fresh weight and number of leaves. Whereas biochemical parameters such as protein content, antioxidative enzymes (catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase), non-enzymatic antioxidants (ascorbic acid, glutathione, tocopherol), osmolytes (proline, carbohydrate), photosynthetic pigments (chlorophyll, carotenoid) and secondary metabolites (phenol, flavonoid, anthocyanin) were estimated on UV-visible spectrophotometer using standard protocols. Further, structural analysis of plant tissue was done using fourier transform infrared spectroscopy spectra (FTIR) and carbon hydrogen nitrogen (CHN) elemental analyzer. Results obtained from the present study revealed significant difference in all morphological and biochemical markers at both 10 and 45 days intervals of time. Further, growth of all plants was found to be directly proportional to the concentration of vermicompost and exposure duration. FTIR spectra and CHN analyses reveal the breakdown of various complex compounds and their transformation from Vcom amended soil to roots of plants. This is the first study in which significant changes were observed in growth, physiology and structural composition of tomato plants at two different exposure periods (10 and 45 days) under glass house conditions which further concluded that vermicompost has a significant potential for increasing plant growth.
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Affiliation(s)
- Raman Tikoria
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, India
| | - Arvinder Kaur
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, India.
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Sentis A, Hemptinne J, Magro A, Outreman Y. Biological control needs evolutionary perspectives of ecological interactions. Evol Appl 2022; 15:1537-1554. [PMID: 36330295 PMCID: PMC9624075 DOI: 10.1111/eva.13457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 05/30/2024] Open
Abstract
While ecological interactions have been identified as determinant for biological control efficiency, the role of evolution remains largely underestimated in biological control programs. With the restrictions on the use of both pesticides and exotic biological control agents (BCAs), the evolutionary optimization of local BCAs becomes central for improving the efficiency and the resilience of biological control. In particular, we need to better account for the natural processes of evolution to fully understand the interactions of pests and BCAs, including in biocontrol strategies integrating human manipulations of evolution (i.e., artificial selection and genetic engineering). In agroecosystems, the evolution of BCAs traits and performance depends on heritable phenotypic variation, trait genetic architecture, selection strength, stochastic processes, and other selective forces. Humans can manipulate these natural processes to increase the likelihood of evolutionary trait improvement, by artificially increasing heritable phenotypic variation, strengthening selection, controlling stochastic processes, or overpassing evolution through genetic engineering. We highlight these facets by reviewing recent studies addressing the importance of natural processes of evolution and human manipulations of these processes in biological control. We then discuss the interactions between the natural processes of evolution occurring in agroecosystems and affecting the artificially improved BCAs after their release. We emphasize that biological control cannot be summarized by interactions between species pairs because pests and biological control agents are entangled in diverse communities and are exposed to a multitude of deterministic and stochastic selective forces that can change rapidly in direction and intensity. We conclude that the combination of different evolutionary approaches can help optimize BCAs to remain efficient under changing environmental conditions and, ultimately, favor agroecosystem sustainability.
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Affiliation(s)
- Arnaud Sentis
- INRAEAix Marseille University, UMR RECOVERAix‐en‐ProvenceFrance
| | - Jean‐Louis Hemptinne
- Laboratoire Évolution et Diversité biologiqueUMR 5174 CNRS/UPS/IRDToulouseFrance
- Université Fédérale de Toulouse Midi‐Pyrénées – ENSFEACastanet‐TolosanFrance
| | - Alexandra Magro
- Laboratoire Évolution et Diversité biologiqueUMR 5174 CNRS/UPS/IRDToulouseFrance
- Université Fédérale de Toulouse Midi‐Pyrénées – ENSFEACastanet‐TolosanFrance
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12
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Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
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Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
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13
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Nansen C. An Interactive Teaching Tool Describing Resistance Evolution and Basic Economics of Insecticide-Based Pest Management. INSECTS 2022; 13:insects13020169. [PMID: 35206742 PMCID: PMC8879777 DOI: 10.3390/insects13020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 12/04/2022]
Abstract
Simple Summary To attract bright, creative, and curious students to the academic fields of applied entomology and sustainable food production, instructors of undergraduate and graduate student courses should discuss experiences with lectures and lab sessions and share effective interactive teaching tools. This communication describes how a simple population model in an Excel spreadsheet can be used in teaching both insecticide resistance evolution and basic economics of insecticide-based pest management. A tutorial video and the model as an Excel spreadsheet are freely available. Through hands-on experience with this and similar interactive teaching tools, students will acquire fundamental knowledge about basic structures population models and they will acquire experience with quantitative data interpretation. Teachers can use this tool and accompanying tutorials to demonstrate how models can be used to describe and visualize complex interactions between insect genetics and crop management. Furthermore, data from published studies can be analyzed and discussed using this interactive teaching tool. Abstract Effective teaching of complex concepts relies heavily on the ability to establish relevance of topics and to engage students in a constructive dialogue. To connect students with abstract concepts and basic theory, instructors foster and facilitate an engaging teaching environment. Population modeling is a cornerstone in applied entomology. However, it is also a topic and skill set that requires both basic mathematical and biological knowledge, and it may be perceived by students as being abstract and exceedingly theoretical. As a way to introduce entomology students at both that undergraduate and graduate levels to hands-on experience with population modeling, a well-established and widely used deterministic genetic population model is presented as an interactive teaching tool. Moreover, the general model describes three genotypes (SS = homozygous susceptible, SR = heterozygous, and RR = homozygous resistant) during 30 discrete and univoltine generations under a shared population density dependence (carrying capacity). Based on user inputs for each genotype (survival, fitness cost, reproductive rate, emigration, and immigration) and an initial resistance allele frequency, model outputs related to resistance evolution are produced. User inputs related to insecticide-based pest management (pest density action threshold, crop damage rate, insecticide treatment costs, and profit potential) can also be introduced to examine and interpret the basic economic effects of different insect pest management scenarios. The proposed model of resistance evolution and basic economics of pest management relies on a large number of important simplifications, so it may only have limited ability to predict the outcomes of real-world (commercial) scenarios. However, as a teaching tool and to introduce students to a well-known and widely used genetic population model structure, the interactive teaching tool is believed to have considerable utility and relevance.
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Affiliation(s)
- Christian Nansen
- Department of Entomology and Nematology, University of California, Davis, CA 95616, USA
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14
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Ravigné V, Becker N, Massol F, Guichoux E, Boury C, Mahé F, Facon B. Fruit fly phylogeny imprints bacterial gut microbiota. Evol Appl 2022; 15:1621-1638. [PMID: 36330298 PMCID: PMC9624087 DOI: 10.1111/eva.13352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
One promising avenue for reconciling the goals of crop production and ecosystem preservation consists in the manipulation of beneficial biotic interactions, such as between insects and microbes. Insect gut microbiota can affect host fitness by contributing to development, host immunity, nutrition, or behavior. However, the determinants of gut microbiota composition and structure, including host phylogeny and host ecology, remain poorly known. Here, we used a well‐studied community of eight sympatric fruit fly species to test the contributions of fly phylogeny, fly specialization, and fly sampling environment on the composition and structure of bacterial gut microbiota. Comprising both specialists and generalists, these species belong to five genera from to two tribes of the Tephritidae family. For each fly species, one field and one laboratory samples were studied. Bacterial inventories to the genus level were produced using 16S metabarcoding with the Oxford Nanopore Technology. Sample bacterial compositions were analyzed with recent network‐based clustering techniques. Whereas gut microbiota were dominated by the Enterobacteriaceae family in all samples, microbial profiles varied across samples, mainly in relation to fly identity and sampling environment. Alpha diversity varied across samples and was higher in the Dacinae tribe than in the Ceratitinae tribe. Network analyses allowed grouping samples according to their microbial profiles. The resulting groups were very congruent with fly phylogeny, with a significant modulation of sampling environment, and with a very low impact of fly specialization. Such a strong imprint of host phylogeny in sympatric fly species, some of which share much of their host plants, suggests important control of fruit flies on their gut microbiota through vertical transmission and/or intense filtering of environmental bacteria.
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Affiliation(s)
| | | | - François Massol
- Univ. Lille CNRS Inserm CHU Lille Institut Pasteur de Lille U1019 ‐ UMR 9017 ‐ CIIL ‐ Center for Infection and Immunity of Lille F‐59000 Lille France
| | | | | | - Frédéric Mahé
- PHIM Plant Health Institute Univ Montpellier CIRAD, INRAE Institut Agro IRD Montpellier France
| | - Benoit Facon
- INRAE UMR CBGP Campus International de Baillarguet F‐349988 Montferrier/Lez France
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15
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Lobos GA, Estrada F, Del Pozo A, Romero-Bravo S, Astudillo CA, Mora-Poblete F. Challenges for a Massive Implementation of Phenomics in Plant Breeding Programs. Methods Mol Biol 2022; 2539:135-157. [PMID: 35895202 DOI: 10.1007/978-1-0716-2537-8_13] [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] [Indexed: 06/15/2023]
Abstract
Due to climate change and expected food shortage in the coming decades, not only will it be necessary to develop cultivars with greater tolerance to environmental stress, but it is also imperative to reduce breeding cycle time. In addition to yield evaluation, plant breeders resort to many sensory assessments and some others of intermediate complexity. However, to develop cultivars better adapted to current/future constraints, it is necessary to incorporate a new set of traits, such as morphophysiological and physicochemical attributes, information relevant to the successful selection of genotypes or parents. Unfortunately, because of the large number of genotypes to be screened, measurements with conventional equipment are unfeasible, especially under field conditions. High-throughput plant phenotyping (HTPP) facilitates collecting a significant amount of data quickly; however, it is necessary to transform all this information (e.g., plant reflectance) into helpful descriptors to the breeder. To the extent that a holistic characterization of the plant (phenomics) is performed in challenging environments, it will be possible to select the best genotypes (forward phenomics) objectively but also understand why the said individual differs from the rest (reverse phenomics). Unfortunately, several elements had prevented phenomics from developing as desired. Consequently, a new set of prediction/validation methodologies, seasonal ambient information, and the fusion of data matrices (e.g., genotypic and phenotypic information) need to be incorporated into the modeling. In this sense, for the massive implementation of phenomics in plant breeding, it will be essential to count an interdisciplinary team that responds to the urgent need to release material with greater capacity to tolerate environmental stress. Therefore, breeding programs should (i) be more efficient (e.g., early discarding of unsuitable material), (ii) have shorter breeding cycles (fewer crosses to achieve the desired cultivar), and (iii) be more productive, increasing the probability of success at the end of the breeding process (percentage of cultivars released to the number of initial crosses).
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Affiliation(s)
- Gustavo A Lobos
- Plant Breeding and Phenomics Center, Faculty of Agricultural Sciences, Universidad de Talca, Talca, Chile.
| | - Félix Estrada
- Plant Breeding and Phenomics Center, Faculty of Agricultural Sciences, Universidad de Talca, Talca, Chile
| | - Alejandro Del Pozo
- Plant Breeding and Phenomics Center, Faculty of Agricultural Sciences, Universidad de Talca, Talca, Chile
| | | | - Cesar A Astudillo
- Department of Computer Science, Faculty of Engineering, Universidad de Talca, Curico, Chile
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16
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Coates A, Johnsen IA, Dempster T, Phillips BL. Parasite management in aquaculture exerts selection on salmon louse behaviour. Evol Appl 2021; 14:2025-2038. [PMID: 34429746 PMCID: PMC8372093 DOI: 10.1111/eva.13255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/18/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022] Open
Abstract
The evolution of pest resistance to management strategies is a major challenge for farmed systems. Mitigating the effects of pest adaptation requires identifying the selective pressures imposed by these strategies. In Atlantic salmon (Salmo salar) aquaculture, barriers are used to prevent salmon louse (Lepeophtheirus salmonis) larvae (copepodids) from entering salmon cages. These barriers are effective against shallow-swimming copepodids, but those swimming deeper can pass underneath and infest salmon. Laboratory experiments suggest that depth regulation in copepodids is a variable behavioural trait with a genetic basis. We used biological-hydrodynamic dispersal models to assess how this trait variation alters the dispersion of lice through the ocean environment and into farms. The dispersal of copepodids with 3 behavioural phenotypes (deep, mean or shallow) was modelled over winter-spring and spring-summer periods in a Norwegian fjord system with intensive aquaculture. The infestation pressure of each phenotype on barrier cages was estimated from their modelled depth distributions: copepodids deeper than 10 m were predicted to successfully pass underneath barriers. The deep phenotype was the most abundant below 10 m and reached infestation pressures 3 times higher than that of the mean phenotype. In contrast, the shallow phenotype infestation pressure reached less than half that of the mean phenotype. These differences in relative fitness indicate that barriers can impose strong directional selection on the swimming behaviour of copepodids. The strength of this selection varied seasonally and geographically, with selection for the deep phenotype stronger in winter-spring and at coastal locations than in spring-summer and within fjords. These findings can be applied across farms to slow louse adaptation, by limiting barriers during situations of strong selection, although this must be balanced against trade-offs to short-term efficacy. More broadly, our study highlights new ways in which dispersal models can address evolutionary questions crucial for sustainable parasite management in aquaculture.
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Affiliation(s)
- Andrew Coates
- Sustainable Aquaculture Laboratory – Temperate and Tropical (SALTT)School of BioSciencesUniversity of MelbourneParkvilleVic.Australia
- Spatial Ecology and Evolution Lab (SPEEL)School of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | | | - Tim Dempster
- Sustainable Aquaculture Laboratory – Temperate and Tropical (SALTT)School of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Ben L. Phillips
- Spatial Ecology and Evolution Lab (SPEEL)School of BioSciencesUniversity of MelbourneParkvilleVic.Australia
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17
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Cao LJ, Li BY, Chen JC, Zhu JY, Hoffmann AA, Wei SJ. Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness. Mol Ecol 2021; 30:4204-4219. [PMID: 34278603 DOI: 10.1111/mec.16055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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18
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Susi H, Laine A. Agricultural land use disrupts biodiversity mediation of virus infections in wild plant populations. THE NEW PHYTOLOGIST 2021; 230:2447-2458. [PMID: 33341977 PMCID: PMC8248426 DOI: 10.1111/nph.17156] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/10/2020] [Indexed: 06/08/2023]
Abstract
Human alteration of natural habitats may change the processes governing species interactions in wild communities. Wild populations are increasingly impacted by agricultural intensification, yet it is unknown whether this alters biodiversity mediation of disease dynamics. We investigated the association between plant diversity (species richness, diversity) and infection risk (virus richness, prevalence) in populations of Plantago lanceolata in natural landscapes as well as those occurring at the edges of cultivated fields. Altogether, 27 P. lanceolata populations were surveyed for population characteristics and sampled for PCR detection of five recently characterized viruses. We find that plant species richness and diversity correlated negatively with virus infection prevalence. Virus species richness declined with increasing plant diversity and richness in natural populations while in agricultural edge populations species richness was moderately higher, and not associated with plant richness. This difference was not explained by changes in host richness between these two habitats, suggesting potential pathogen spill-over and increased transmission of viruses across the agro-ecological interface. Host population connectivity significantly decreased virus infection prevalence. We conclude that human use of landscapes may change the ecological laws by which natural communities are formed with far reaching implications for ecosystem functioning and disease.
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Affiliation(s)
- Hanna Susi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 65Helsinki00014Finland
| | - Anna‐Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 65Helsinki00014Finland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
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19
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Ganie ZA, Obrigawitch T, Kang IH, Copeland D, Gutteridge S, May J, Schrage B, Albright R, Chandi A. An outlook of FMC's current and future herbicide-resistance management strategies. PEST MANAGEMENT SCIENCE 2021; 77:1559-1563. [PMID: 32309902 DOI: 10.1002/ps.5865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/05/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Herbicide resistance has emerged globally as a serious threat to profitable crop production. FMC promotes integrated weed management approaches including responsible use of existing herbicides, use of non-herbicide weed control tools, awareness about herbicide resistance issues, and support to herbicide resistance management initiatives. FMC is dedicated to developing sustainable weed control solutions through the discovery of new herbicides with novel sites-of-action, effective formulations, advanced application technology, and proactive monitoring for herbicide resistance. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Zahoor A Ganie
- Stine Research Center, FMC Corporation, Elkton, Delaware
| | | | - Il-Ho Kang
- Stine Research Center, FMC Corporation, Elkton, Delaware
| | - Drake Copeland
- Stine Research Center, FMC Corporation, Elkton, Delaware
| | | | - John May
- Stine Research Center, FMC Corporation, Elkton, Delaware
| | | | | | - Aman Chandi
- Stine Research Center, FMC Corporation, Elkton, Delaware
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20
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Sang Y, Mejuto JC, Xiao J, Simal-Gandara J. Assessment of Glyphosate Impact on the Agrofood Ecosystem. PLANTS (BASEL, SWITZERLAND) 2021; 10:405. [PMID: 33672572 PMCID: PMC7924050 DOI: 10.3390/plants10020405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
Agro-industries should adopt effective strategies to use agrochemicals such as glyphosate herbicides cautiously in order to protect public health. This entails careful testing and risk assessment of available choices, and also educating farmers and users with mitigation strategies in ecosystem protection and sustainable development. The key to success in this endeavour is using scientific research on biological pest control, organic farming and regulatory control, etc., for new developments in food production and safety, and for environmental protection. Education and research is of paramount importance for food and nutrition security in the shadow of climate change, and their consequences in food production and consumption safety and sustainability. This review, therefore, diagnoses on the use of glyphosate and the associated development of glyphosate-resistant weeds. It also deals with the risk assessment on human health of glyphosate formulations through environment and dietary exposures based on the impact of glyphosate and its metabolite AMPA-(aminomethyl)phosphonic acid-on water and food. All this to setup further conclusions and recommendations on the regulated use of glyphosate and how to mitigate the adverse effects.
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Affiliation(s)
- Yaxin Sang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China;
| | - Juan-Carlos Mejuto
- Department of Physical Chemistry, Faculty of Science, University of Vigo—Ourense Campus, E32004 Ourense, Spain;
| | - Jianbo Xiao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
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21
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Rani L, Thapa K, Kanojia N, Sharma N, Singh S, Grewal AS, Srivastav AL, Kaushal J. An extensive review on the consequences of chemical pesticides on human health and environment. JOURNAL OF CLEANER PRODUCTION 2021. [PMID: 0 DOI: 10.1016/j.jclepro.2020.124657] [Citation(s) in RCA: 287] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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22
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David L, Kang J, Dufresne D, Zhu D, Chen S. Multi-Omics Revealed Molecular Mechanisms Underlying Guard Cell Systemic Acquired Resistance. Int J Mol Sci 2020; 22:ijms22010191. [PMID: 33375472 PMCID: PMC7795379 DOI: 10.3390/ijms22010191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 01/09/2023] Open
Abstract
Systemic Acquired Resistance (SAR) improves immunity of plant systemic tissue after local exposure to a pathogen. Guard cells that form stomatal pores on leaf surfaces recognize bacterial pathogens via pattern recognition receptors, such as Flagellin Sensitive 2 (FLS2). However, how SAR affects stomatal immunity is not known. In this study, we aim to reveal molecular mechanisms underlying the guard cell response to SAR using multi-omics of proteins, metabolites and lipids. Arabidopsis plants previously exposed to pathogenic bacteria Pseudomonas syringae pv. tomato DC3000 (Pst) exhibit an altered stomatal response compared to control plants when they are later exposed to the bacteria. Reduced stomatal apertures of SAR primed plants lead to decreased number of bacteria in leaves. Multi-omics has revealed molecular components of SAR response specific to guard cells functions, including potential roles of reactive oxygen species (ROS) and fatty acid signaling. Our results show an increase in palmitic acid and its derivative in the primed guard cells. Palmitic acid may play a role as an activator of FLS2, which initiates stomatal immune response. Improved understanding of how SAR signals affect stomatal immunity can aid biotechnology and marker-based breeding of crops for enhanced disease resistance.
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Affiliation(s)
- Lisa David
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (L.D.); (J.K.); (D.Z.)
- Genetics Institute (UFGI), University of Florida, Gainesville, FL 32610, USA
| | - Jianing Kang
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (L.D.); (J.K.); (D.Z.)
- Genetics Institute (UFGI), University of Florida, Gainesville, FL 32610, USA
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Daniel Dufresne
- Department of Chemistry, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Dan Zhu
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (L.D.); (J.K.); (D.Z.)
- Genetics Institute (UFGI), University of Florida, Gainesville, FL 32610, USA
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (L.D.); (J.K.); (D.Z.)
- Genetics Institute (UFGI), University of Florida, Gainesville, FL 32610, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL 32610, USA
- Correspondence: ; Tel.: +1-352-273-8330
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23
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Karlsson Green K, Stenberg JA, Lankinen Å. Making sense of Integrated Pest Management (IPM) in the light of evolution. Evol Appl 2020; 13:1791-1805. [PMID: 32908586 PMCID: PMC7463341 DOI: 10.1111/eva.13067] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Integrated Pest Management (IPM) is a holistic approach to combat pests (including herbivores, pathogens, and weeds) using a combination of preventive and curative actions, and only applying synthetic pesticides when there is an urgent need. Just as the recent recognition that an evolutionary perspective is useful in medicine to understand and predict interactions between hosts, diseases, and medical treatments, we argue that it is crucial to integrate an evolutionary framework in IPM to develop efficient and reliable crop protection strategies that do not lead to resistance development in herbivores, pathogens, and weeds. Such a framework would not only delay resistance evolution in pests, but also optimize each element of the management and increase the synergies between them. Here, we outline key areas within IPM that would especially benefit from a thorough evolutionary understanding. In addition, we discuss the difficulties and advantages of enhancing communication among research communities rooted in different biological disciplines and between researchers and society. Furthermore, we present suggestions that could advance implementation of evolutionary principles in IPM and thus contribute to the development of sustainable agriculture that is resilient to current and emerging pests.
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Affiliation(s)
- Kristina Karlsson Green
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Johan A. Stenberg
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Åsa Lankinen
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
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24
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Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla-Ramírez M, Dicke M, Fatouros NE, González-Cabrera J, Groot TVM, Haye T, Knapp M, Koskinioti P, Le Hesran S, Lyrakis M, Paspati A, Pérez-Hedo M, Plouvier WN, Schlötterer C, Stahl JM, Thiel A, Urbaneja A, van de Zande L, Verhulst EC, Vet LEM, Visser S, Werren JH, Xia S, Zwaan BJ, Magalhães S, Beukeboom LW, Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol Rev Camb Philos Soc 2020; 95:1838-1854. [PMID: 32794644 PMCID: PMC7689903 DOI: 10.1111/brv.12641] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro‐ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker‐assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post‐release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Erica Ras
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Kim B Ferguson
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Simone Ariëns
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | | | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Jacques Brodeur
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Quebec, Canada, H1X 2B2
| | - Margreet A Bruins
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alejandra Centurión
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Sophie R Chattington
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Milena Chinchilla-Ramírez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joel González-Cabrera
- Department of Genetics, Estructura de Recerca Interdisciplinar en Biotecnología i Biomedicina (ERI-BIOTECMED), Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Universitat de València, Dr Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Thomas V M Groot
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Tim Haye
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland
| | - Markus Knapp
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Panagiota Koskinioti
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Sophie Le Hesran
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Manolis Lyrakis
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Angeliki Paspati
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Wouter N Plouvier
- INRA, CNRS, UMR 1355-7254, 400 Route des Chappes, BP 167 06903, Sophia Antipolis Cedex, France
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Judith M Stahl
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland.,Kearney Agricultural Research and Extension Center, University of California Berkeley, 9240 South Riverbend Avenue, Parlier, CA, 93648, USA
| | - Andra Thiel
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Eveline C Verhulst
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Louise E M Vet
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Sander Visser
- Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Shuwen Xia
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016, Lisbon, Portugal
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Bart A Pannebakker
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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25
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Reynolds BA, Oli MW, Oli MK. Eco-oncology: Applying ecological principles to understand and manage cancer. Ecol Evol 2020; 10:8538-8553. [PMID: 32884638 PMCID: PMC7452771 DOI: 10.1002/ece3.6590] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is a disease of single cells that expresses itself at the population level. The striking similarities between initiation and growth of tumors and dynamics of biological populations, and between metastasis and ecological invasion and community dynamics suggest that oncology can benefit from an ecological perspective to improve our understanding of cancer biology. Tumors can be viewed as complex, adaptive, and evolving systems as they are spatially and temporally heterogeneous, continually interacting with each other and with the microenvironment and evolving to increase the fitness of the cancer cells. We argue that an eco-evolutionary perspective is essential to understand cancer biology better. Furthermore, we suggest that ecologically informed therapeutic approaches that combine standard of care treatments with strategies aimed at decreasing the evolutionary potential and fitness of neoplastic cells, such as disrupting cell-to-cell communication and cooperation, and preventing successful colonization of distant organs by migrating cancer cells, may be effective in managing cancer as a chronic condition.
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Affiliation(s)
- Brent A. Reynolds
- Department of NeurosurgeryCollege of MedicineUniversity of FloridaGainesvilleFLUSA
| | - Monika W. Oli
- Department of Microbiology and Cell ScienceInstitute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFLUSA
| | - Madan K. Oli
- Department of Wildlife Ecology and ConservationInstitute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFLUSA
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26
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Huang Z, Cui H, Wang C, Wu T, Zhang C, Huang H, Wei S. Investigation of resistance mechanism to fomesafen in Amaranthus retroflexus L. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 165:104560. [PMID: 32359536 DOI: 10.1016/j.pestbp.2020.104560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Amaranthus retroflexus L. is one of the most troublesome weeds in autumn-crop fields in Northeast China. In recent years, field applications of fomesafen have failed to control an A. retroflexus population in Heilongjiang Province, China. Therefore, in this study, experiments were conducted to determine the resistance of A. retroflexus to fomesafen and investigate the molecular basis of herbicide resistance. Whole-plant dose-response experiments showed that the resistant (R) population exhibited 41.8-fold resistance to fomesafen compared with the susceptible (S) population. Target-gene sequence analysis revealed an Arg-128-Gly substitution in the protoporphyrinogen oxidase (PPO) in the R population. The response of PPO2 transgenic Arabidopsis thaliana to fomesafen demonstrated that the Arg-128-Gly substitution conferred high resistance to fomesafen. Cross- and multiple-resistance analyses indicated that the R population was cross-resistant to lactofen and carfentrazone-ethyl but was sensitive to imazethapyr, thifensulfuron-methyl, atrazine, and glyphosate. This study indicated that the Arg-128-Gly substitution is the main reason for A. retroflexus resistance to fomesafen. To our knowledge, this is the first report of a target-site based mechanism for the resistance to a PPO-inhibiting herbicide in A. retroflexus.
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Affiliation(s)
- Zhaofeng Huang
- Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), 100193, China
| | - Hailan Cui
- Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), 100193, China
| | - Chunyu Wang
- College of Agriculture, Northeast Agricultural University, 150030, China
| | - Tong Wu
- College of Agriculture, Northeast Agricultural University, 150030, China
| | - Chaoxian Zhang
- Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), 100193, China
| | - Hongjuan Huang
- Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), 100193, China
| | - Shouhui Wei
- Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), 100193, China.
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27
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Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide. SUSTAINABILITY 2020. [DOI: 10.3390/su12031188] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fungicide is one of the main approaches used in agriculture to manage plant diseases for food production, but their effectiveness can be reduced due to the evolution of plant pathogens. Understanding the genetics and evolutionary processes responsible for the development of fungicide resistance is a key to food production and social sustainability. In this study, we used a common garden experiment to examine the source of genetic variation, natural selection, and temperature contributing to the development of azoxystrobin resistance in Phytophthora infestans and infer sustainable ways of plant disease management in future. We found that plasticity contributed to ~40% of phenotypic variation in azoxystrobin sensitivity while heritability accounted for 16%. Further analysis indicated that overall population differentiation in azoxystrobin sensitivity (QST) was significantly greater than the overall population differentiation in simple sequence repeat (SSR) marker (FST), and the P. infestans isolates demonstrated higher level of azoxystrobin sensitivity at the higher experimental temperature. These results suggest that changes in target gene expression, enzymatic activity, or metabolic rate of P. infestans play a more important role in the adaptation of the pathogen to azoxystrobin resistance than that of mutations in target genes. The development of azoxystrobin resistance in P. infestans is likely driven by diversifying selection for local adaptation, and elevated temperature associated with global warming in the future may increase the effectiveness of using azoxystrobin to manage P. infestans. The sustainable approaches for increasing disease control effectiveness and minimizing the erosion of the fungicide efficacy are proposed.
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28
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Bargués-Ribera M, Gokhale CS. Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations. PLoS Comput Biol 2020; 16:e1007546. [PMID: 31945057 PMCID: PMC6964815 DOI: 10.1371/journal.pcbi.1007546] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
Since its origins, thousands of years ago, agriculture has been challenged by the presence of evolving plant pathogens. Temporal rotations of host and non-host crops have helped farmers to control epidemics among other utilities, but further efforts for strategy assessment are needed. Here, we present a methodology for developing crop rotation strategies optimal for control of pathogens informed by numerical simulations of eco-evolutionary dynamics in one field. This approach can integrate agronomic criteria used in crop rotations—soil quality and cash yield—and the analysis of pathogen evolution in systems where hosts are artificially selected. Our analysis shows which rotation patterns perform better in maximising crop yield when an unspecified infection occurs, with yield being dependent on both soil quality and the strength of the epidemic. Importantly, the use of non-host crops, which both improve soil quality and control the epidemic results in similar rational rotation strategies for diverse agronomic and infection conditions. We test the repeatability of the best rotation patterns over multiple decades, an essential end-user goal. Our results provide sustainable strategies for optimal resource investment for increased food production and lead to further insights into the minimisation of pesticide use in a society demanding ever more efficient agriculture. The invention of agriculture is a major evolutionary transition in the social evolution of the human race. Transforming the lifestyle from nomadic to sedentary, agriculture provided humankind with the stability necessary to make rapid advancements. However, agriculture, as we know it, is now in danger. While agriculture is a grand artificial selection experiment, it is in a constant battle with the brute force of natural selection, generating highly infectious plant pathogens. Traditional techniques such as slash-burn techniques are not sustainable for feeding the ever-increasing population. Crop rotation, on the other hand, has been developed over thousands of years as a sustainable method. We provide a computational model of how crop rotations can be used to tackle pathogen infection and what properties of rotation patterns make them sustainable in the long run. We hope that this study, together with other sustainable methods such as minimal pesticide use and biocontrol, can make agriculture more efficient.
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Affiliation(s)
- Maria Bargués-Ribera
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Chaitanya S. Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
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29
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Ewing PM, Runck BC, Kono TYJ, Kantar MB. The home field advantage of modern plant breeding. PLoS One 2019; 14:e0227079. [PMID: 31877180 PMCID: PMC6932805 DOI: 10.1371/journal.pone.0227079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/10/2019] [Indexed: 12/03/2022] Open
Abstract
Since the mid-20th century, crop breeding has driven unprecedented yield gains. Breeders generally select for broadly- and reliably-performing varieties that display little genotype-by-environment interaction (GxE). In contrast, ecological theory predicts that across environments that vary spatially or temporally, the most productive population will be a mixture of narrowly adapted specialists. We quantified patterns of broad and narrow adaptation in modern, commercial maize (Zea mays L.) hybrids planted across 216 site-years, from 1999–2018, for the University of Illinois yield trials. We found that location was the dominant source of yield variation (44.5%), and yearly weather was the smallest (1.7%), which suggested a benefit for reliable performance in narrow biophysical environments. Varieties displayed a large “home field advantage” when growing in the location of best performance relative to other varieties. Home field advantage accounted for 19% of GxE and provided a yield increase of 1.01 ± 0.04 Mg ∙ ha-1 (7.6% relative to mean yield), yet was both smaller than predicted by a null model and unchanged across time. This counterfactual suggests that commercial breeding programs have missed an opportunity to further increase yields by leveraging local adaptation. Public breeding programs may pursue this opportunity by releasing specialist varieties that perform reliably in narrow environments. As seed sources are increasingly privatized and consolidated, this alternate strategy may compliment private breeding to support global food security.
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Affiliation(s)
- Patrick M. Ewing
- Department of Crop, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Bryan C. Runck
- GEMS Agroinformatics Initiative, University of Minnesota, Minneapolis, MN, United States of America
| | - Thomas Y. J. Kono
- Minnesota Supercomputing Institute, Minneapolis, MN, United States of America
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Science, University of Hawaii at Manoa, Honolulu, HI, United States of America
- * E-mail:
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30
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Missbah El Idrissi M, Lamin H, ElFaik S, Tortosa G, Peix A, Bedmar E, Abdelmoumen H. Microvirga
sp. symbiovar mediterranense nodulates
Lupinus cosentinii
grown wild in Morocco. J Appl Microbiol 2019; 128:1109-1118. [DOI: 10.1111/jam.14526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- M. Missbah El Idrissi
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - H. Lamin
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - S. ElFaik
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - G. Tortosa
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - A. Peix
- Instituto de Recursos Naturales y Agrobiología IRNASA‐CSIC Salamanca Spain
| | - E.J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - H. Abdelmoumen
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
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31
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Besset-Manzoni Y, Joly P, Brutel A, Gerin F, Soudière O, Langin T, Prigent-Combaret C. Does in vitro selection of biocontrol agents guarantee success in planta? A study case of wheat protection against Fusarium seedling blight by soil bacteria. PLoS One 2019; 14:e0225655. [PMID: 31805068 PMCID: PMC6894788 DOI: 10.1371/journal.pone.0225655] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/09/2019] [Indexed: 01/14/2023] Open
Abstract
Biological control is a great hope for reducing the overutilization of pesticides in agricultural soils. It often involves microorganisms or molecules produced by microorganisms that will be able to interact with either a plant or pathogens of this plant to reduce the growth of the pathogen and limit its negative impact on the host plant. When new biocontrol products are developed, strains were mostly selected based on their ability to inhibit a pathogen of interest under in vitro conditions via antagonistic effects. Strains with no in vitro effect are often discarded and not tested in planta. But is the in vitro selection of bacterial agents according to their antagonism activities towards a plant pathogen the best way to get effective biocontrol products? To answer this question, we used wheat and the fungal pathogen Fusarium graminearum as a study pathosystem model. A library of 205 soil bacteria was screened in 2 types of in vitro growth inhibition tests against F. graminearum, and in an in planta experiment. We find strains which do not have inhibition phenotypes in vitro but good efficacy in planta. Interestingly, some strains belong to species (Microbacterium, Arthrobacter, Variovorax) that are not known in the literature for their ability to protect plants against fungal pathogens. Thus, developing a biocontrol product against F. graminearum must be preferentially based on the direct screening of strains for their protective activity on wheat plants against fungal diseases, rather than on their in vitro antagonistic effects on fungal growth.
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Affiliation(s)
- Yoann Besset-Manzoni
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne cedex, France
- Biovitis, Le Bourg, Saint Etienne-de-Chomeil, France
| | - Pierre Joly
- Biovitis, Le Bourg, Saint Etienne-de-Chomeil, France
| | - Aline Brutel
- Biovitis, Le Bourg, Saint Etienne-de-Chomeil, France
| | - Florence Gerin
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne cedex, France
| | - Olivier Soudière
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont–Ferrand, France
| | - Thierry Langin
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont–Ferrand, France
| | - Claire Prigent-Combaret
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne cedex, France
- * E-mail:
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32
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Zhang X, Liu B, Zou F, Shen D, Yin Z, Wang R, He F, Wang Y, Tyler BM, Fan W, Qian W, Dou D. Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae. Front Microbiol 2019; 10:2792. [PMID: 31849921 PMCID: PMC6895562 DOI: 10.3389/fmicb.2019.02792] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022] Open
Abstract
Due to the monocultural basis of agricultural crops, mutated plant microbes with increased pathogenicity can easily spread in the field and lead to serious yield losses. As a major threat to a wide range of crop plants, oomycete pathogens continuously undergo adaptive evolution to overcome plant defense barriers. However, the genetic basis of their evolution at the molecular level remains largely unknown. Here, we investigated the nature variation and the population genomics of the soybean pathogen Phytophthora sojae by high-throughput genome re-sequencing. Genomic variation analysis revealed uneven “two-speed” evolutionary pattern with genes in gene-sparse regions (GSRs) showing higher rates of structural polymorphisms and positive selection. GSRs are enriched in effector genes and transposase-related genes. Our results also suggested that the NADH oxidase and MIP transporter gene families undergo rapid and diversifying selection. Furthermore, we demonstrated that P. sojae isolates possess varying numbers of RxLR effectors with diverse sequences, totaling 471 members. Among them, 42 core RxLR effectors are assumed to be important for infection. Finally, we observed that Avr genes exhibit abundant sequence variation in P. sojae isolates. Several novel variants lead to the evading of host resistance, including a complete deletion in Avr3c and amino acid mutations in Avr1a. Taken together, our results provide an adaptive landscape of P. sojae at single-nucleotide resolution, as well as resources for further resistance breeding and disease prevention against this important plant pathogen.
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Affiliation(s)
- Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Bo Liu
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fen Zou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyuan Yin
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Rongbo Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Feng He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Wei Fan
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wanqiang Qian
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
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33
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Wei S, He X, Wang D, Xiang J, Yang Y, Yuan S, Shang J, Yang H. Genetic structure and variability of tobacco vein banding mosaic virus populations. Arch Virol 2019; 164:2459-2467. [PMID: 31286220 DOI: 10.1007/s00705-019-04342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
Abstract
Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC). Further analysis indicated that the spatial genetic structure of TVBMV populations is likely to have been caused by natural selection. Phylogeographic analysis provided strong support for spatial diffusion pathways between the Southwest and Northwest tobacco-producing regions. The TVBMV CP gene was found to be under negative selection, and no significant positive selection of amino acids was detected in the SW group; however, the isolates of the MC group experienced significant positive selection pressure at the first and third amino acid sites of CP. This study suggests that natural selection and habitat heterogeneity are important evolutionary mechanisms affecting the genetic structure of the TVBMV population.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorong He
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Die Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinyou Xiang
- Sichuan Tobacco Company Yibin Company, Yibin, 644000, China
| | - Yide Yang
- Sichuan Tobacco Company Yibin Company, Yibin, 644000, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University Chengdu Campus, Chengdu, 611130, China
| | - Jing Shang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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Dumont F, Réale D, Lucas É. Can Isogroup Selection of Highly Zoophagous Lines of a Zoophytophagous Bug Improve Biocontrol of Spider Mites in Apple Orchards? INSECTS 2019; 10:insects10090303. [PMID: 31540397 PMCID: PMC6780391 DOI: 10.3390/insects10090303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/29/2022]
Abstract
Zoophytophagous predators provide benefits in agroecosystems when feeding on pests, but they can also cause crop damage. Optimizing the use of zoophytophagous predators as biocontrol agents would require improving pest control and/or limiting damage. Populations of a zoophytophagous species can be composed of a mix of individuals diverging in their level of diet specialization. Consequently, depending on their level of zoophagy, individuals would vary widely in the benefits and risks they provide to pest management. We tested the hypothesis that manipulating the composition of the population of a zoophytophagous insect, the mullein bug, Campylomma verbasci (Hemiptera: Miridae), towards an increased zoophagy would increase their net benefit in an apple orchard. We compared the inherent benefits and risks of two different isogroup lines of mullein bug that genetically differed in their level of zoophagy. In spring, when damage occurs, both strains infrequently punctured apple fruit, which rarely lead to damage and therefore represented a low risk. During summer, only the highly-zoophagous line impacted the spider mite population, while the lowly-zoophagous line did not differ from the control treatments. We concluded that manipulating the composition of the zoophytophagous predator population provided extra net benefits that improved pest control.
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Affiliation(s)
- François Dumont
- Département des Sciences Biologiques, Université du Québec à Montréal, CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada.
| | - Denis Réale
- Département des Sciences Biologiques, Université du Québec à Montréal, CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada.
| | - Éric Lucas
- Département des Sciences Biologiques, Université du Québec à Montréal, CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada.
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Pruvost O, Boyer K, Ravigné V, Richard D, Vernière C. Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity. Evol Appl 2019; 12:1523-1538. [PMID: 31462912 PMCID: PMC6708428 DOI: 10.1111/eva.12788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/25/2019] [Accepted: 02/24/2019] [Indexed: 12/15/2022] Open
Abstract
Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.
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Affiliation(s)
| | | | | | - Damien Richard
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- ANSESSaint Pierre, La RéunionFrance
- Université de la RéunionUMR PVBMTSaint Denis, La RéunionFrance
| | - Christian Vernière
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- CIRADUMR BGPIMontpellierFrance
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36
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Climate Change Impacts and Adaptation Strategies of Agriculture in Mediterranean-Climate Regions (MCRs). SUSTAINABILITY 2019. [DOI: 10.3390/su11102769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The world’s five Mediterranean-climate regions (MCRs) share unique climatic regimes of mild, wet winters and warm and dry summers. Agriculture in these regions is threatened by increases in the occurrence of drought and high temperature events associated with climate change (CC). In this review we analyze what would be the effects of CC on crops (including orchards and vineyards), how crops and cropping and farming systems could adapt to CC, and what are the social and economic impacts, as well as the strategies used by producers to adapt to CC. In rainfed areas, water deficit occurs mostly during the flowering and grain filling stages (terminal drought stress), which has large detrimental effects on the productivity of crops. Orchards and vineyards, which are mostly cultivated in irrigated areas, will also be vulnerable to water deficit due to a reduction in water available for irrigation and an increase in evapotranspiration. Adaptation of agriculture to CC in MCRs requires integrated strategies that encompass different levels of organization: the crop (including orchards and vineyards), the cropping system (sequence of crops and management techniques used on a particular agricultural field) and the farming system, which includes the farmer.
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37
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Masini L, Grenville‐Briggs LJ, Andreasson E, Råberg L, Lankinen Å. Tolerance and overcompensation to infection by Phytophthora infestans in the wild perennial climber Solanum dulcamara. Ecol Evol 2019; 9:4557-4567. [PMID: 31031927 PMCID: PMC6476776 DOI: 10.1002/ece3.5057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/16/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
Studies of infection by Phytophthora infestans-the causal agent of potato late blight-in wild species can provide novel insights into plant defense responses, and indicate how wild plants might be influenced by recurrent epidemics in agricultural fields. In the present study, our aim was to investigate if different clones of Solanum dulcamara (a relative of potato) collected in the wild differ in resistance and tolerance to infection by a common European isolate of P. infestans. We performed infection experiments with six S. dulcamara genotypes (clones) both in the laboratory and in the field and measured the degree of infection and plant performance traits. In the laboratory, the six evaluated genotypes varied from resistant to susceptible, as measured by degree of infection 20 days post infection. Two of the four genotypes susceptible to infection showed a quadratic (concave downward) relationship between the degree of infection and shoot length, with maximum shoot length at intermediate values of infection. This result suggests overcompensation, that is, an increase in growth in infected individuals. The number of leaves decreased with increasing degree of infection, but at different rates in the four susceptible genotypes, indicating genetic variation for tolerance. In the field, the inoculated genotypes did not show any disease symptoms, but plant biomass at the end of the growing season was higher for inoculated plants than for controls, in-line with the overcompensation detected in the laboratory. We conclude that in S. dulcamara there are indications of genetic variation for both resistance and tolerance to P. infestans infection. Moreover, some genotypes displayed overcompensation. Learning about plant tolerance and overcompensation to infection by pathogens can help broaden our understanding of plant defense in natural populations and help develop more sustainable plant protection strategies for economically important crop diseases.
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Affiliation(s)
- Laura Masini
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- Present address:
British American TobaccoPlant Biotechnology DivisionCambridgeUK
| | | | - Erik Andreasson
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Lars Råberg
- Department of BiologyLund UniversityLundSweden
| | - Åsa Lankinen
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
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38
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Dumont F, Aubry O, Lucas E. From Evolutionary Aspects of Zoophytophagy to Biological Control. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00221] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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39
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Bagavathiannan MV, Davis AS. An ecological perspective on managing weeds during the great selection for herbicide resistance. PEST MANAGEMENT SCIENCE 2018; 74:2277-2286. [PMID: 29569406 DOI: 10.1002/ps.4920] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 05/10/2023]
Abstract
More than 70 years after modern agriculture declared a 'war on weeds', they continue to thrive and suppress crop yields. Viewing weeds as an enemy that can be defeated if only a powerful enough technology can be deployed is a losing proposition. The latest evidence for the inadequacy of this approach, rampant evolution of multiple herbicide-resistant weed genotypes and dwindling options for chemical control in many production systems, should be seen as an urgent message to all those concerned with the science and practice of weed management: we need another way of thinking about the weed resistance issue. Fortunately, the theoretical and practical foundation of this alternative approach, ecological weed management, has been in development for decades. Here, we use Barry Commoner's laws of ecology as a conceptual frame for a review of some of the fundamental concepts of ecological weed management. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | - Adam S Davis
- United States Department of Agriculture-Agricultural Research Service, Global Change and Photosynthesis Research Unit, Urbana, Illinois, USA
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40
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Papaïx J, Rimbaud L, Burdon JJ, Zhan J, Thrall PH. Differential impact of landscape-scale strategies for crop cultivar deployment on disease dynamics, resistance durability and long-term evolutionary control. Evol Appl 2018; 11:705-717. [PMID: 29875812 PMCID: PMC5979631 DOI: 10.1111/eva.12570] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/23/2017] [Indexed: 01/28/2023] Open
Abstract
A multitude of resistance deployment strategies have been proposed to tackle the evolutionary potential of pathogens to overcome plant resistance. In particular, many landscape-based strategies rely on the deployment of resistant and susceptible cultivars in an agricultural landscape as a mosaic. However, the design of such strategies is not easy as strategies targeting epidemiological or evolutionary outcomes may not be the same. Using a stochastic spatially explicit model, we studied the impact of landscape organization (as defined by the proportion of fields cultivated with a resistant cultivar and their spatial aggregation) and key pathogen life-history traits on three measures of disease control. Our results show that short-term epidemiological dynamics are optimized when landscapes are planted with a high proportion of the resistant cultivar in low aggregation. Importantly, the exact opposite situation is optimal for resistance durability. Finally, well-mixed landscapes (balanced proportions with low aggregation) are optimal for long-term evolutionary equilibrium (defined here as the level of long-term pathogen adaptation). This work offers a perspective on the potential for contrasting effects of landscape organization on different goals of disease management and highlights the role of pathogen life history.
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Affiliation(s)
| | | | | | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
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41
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Abstract
Insect pests are responsible for substantial crop losses worldwide through direct damage and transmission of plant diseases, and novel approaches that complement or replace broad-spectrum chemical insecticides will facilitate the sustainable intensification of food production in the coming decades. Multiple strategies for improved crop resistance to insect pests, especially strategies relating to plant secondary metabolism and immunity and microbiome science, are becoming available. Recent advances in metabolic engineering of plant secondary chemistry offer the promise of specific toxicity or deterrence to insect pests; improved understanding of plant immunity against insects provides routes to optimize plant defenses against insects; and the microbiomes of insect pests can be exploited, either as a target or as a vehicle for delivery of insecticidal agents. Implementation of these advances will be facilitated by ongoing advances in plant breeding and genetic technologies.
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Affiliation(s)
- Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
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42
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Pélissié B, Crossley MS, Cohen ZP, Schoville SD. Rapid evolution in insect pests: the importance of space and time in population genomics studies. CURRENT OPINION IN INSECT SCIENCE 2018; 26:8-16. [PMID: 29764665 DOI: 10.1016/j.cois.2017.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/28/2017] [Accepted: 12/31/2017] [Indexed: 06/08/2023]
Abstract
Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems.
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Affiliation(s)
- Benjamin Pélissié
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA.
| | - Michael S Crossley
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
| | - Zachary Paul Cohen
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
| | - Sean D Schoville
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
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43
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Feckler A, Goedkoop W, Konschak M, Bundschuh R, Kenngott KGJ, Schulz R, Zubrod JP, Bundschuh M. History matters: Heterotrophic microbial community structure and function adapt to multiple stressors. GLOBAL CHANGE BIOLOGY 2018; 24:e402-e415. [PMID: 28787754 DOI: 10.1111/gcb.13859] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/31/2017] [Indexed: 05/28/2023]
Abstract
Ecosystem functions in streams (e.g., microbially mediated leaf litter breakdown) are threatened globally by the predicted agricultural intensification and its expansion into pristine areas, which is associated with increasing use of fertilizers and pesticides. However, the ecological consequences may depend on the disturbance history of microbial communities. To test this, we assessed the effects of fungicides and nutrients (four levels each) on the structural and functional resilience of leaf-associated microbial communities with differing disturbance histories (pristine vs. previously disturbed) in a 2 × 4 × 4-factorial design (n = 6) over 21 days. Microbial leaf breakdown was assessed as a functional variable, whereas structural changes were characterized by the fungal community composition, species richness, biomass, and other factors. Leaf breakdown by the pristine microbial community was reduced by up to 30% upon fungicide exposure compared with controls, whereas the previously disturbed microbial community increased leaf breakdown by up to 85%. This significant difference in the functional response increased in magnitude with increasing nutrient concentrations. A pollution-induced community tolerance in the previously disturbed microbial community, which was dominated by a few species with high breakdown efficacies, may explain the maintained function under stress. Hence, the global pressure on pristine ecosystems by agricultural expansion is expected to cause a modification in the structure and function of heterotrophic microbial communities, with microbially mediated leaf litter breakdown likely becoming more stable over time as a consequence of fungal community adaptions.
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Affiliation(s)
- Alexander Feckler
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Willem Goedkoop
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marco Konschak
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
| | - Rebecca Bundschuh
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
| | - Kilian G J Kenngott
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
| | - Ralf Schulz
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
| | - Jochen P Zubrod
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
| | - Mirco Bundschuh
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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44
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Iriondo JM, Milla R, Volis S, Rubio de Casas R. Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:78-88. [PMID: 28976618 DOI: 10.1111/plb.12640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/27/2017] [Indexed: 05/12/2023]
Abstract
Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture.
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Affiliation(s)
- J M Iriondo
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - R Milla
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - S Volis
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - R Rubio de Casas
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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45
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Brilli L, Bechini L, Bindi M, Carozzi M, Cavalli D, Conant R, Dorich CD, Doro L, Ehrhardt F, Farina R, Ferrise R, Fitton N, Francaviglia R, Grace P, Iocola I, Klumpp K, Léonard J, Martin R, Massad RS, Recous S, Seddaiu G, Sharp J, Smith P, Smith WN, Soussana JF, Bellocchi G. Review and analysis of strengths and weaknesses of agro-ecosystem models for simulating C and N fluxes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:445-470. [PMID: 28454025 DOI: 10.1016/j.scitotenv.2017.03.208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 05/21/2023]
Abstract
Biogeochemical simulation models are important tools for describing and quantifying the contribution of agricultural systems to C sequestration and GHG source/sink status. The abundance of simulation tools developed over recent decades, however, creates a difficulty because predictions from different models show large variability. Discrepancies between the conclusions of different modelling studies are often ascribed to differences in the physical and biogeochemical processes incorporated in equations of C and N cycles and their interactions. Here we review the literature to determine the state-of-the-art in modelling agricultural (crop and grassland) systems. In order to carry out this study, we selected the range of biogeochemical models used by the CN-MIP consortium of FACCE-JPI (http://www.faccejpi.com): APSIM, CERES-EGC, DayCent, DNDC, DSSAT, EPIC, PaSim, RothC and STICS. In our analysis, these models were assessed for the quality and comprehensiveness of underlying processes related to pedo-climatic conditions and management practices, but also with respect to time and space of application, and for their accuracy in multiple contexts. Overall, it emerged that there is a possible impact of ill-defined pedo-climatic conditions in the unsatisfactory performance of the models (46.2%), followed by limitations in the algorithms simulating the effects of management practices (33.1%). The multiplicity of scales in both time and space is a fundamental feature, which explains the remaining weaknesses (i.e. 20.7%). Innovative aspects have been identified for future development of C and N models. They include the explicit representation of soil microbial biomass to drive soil organic matter turnover, the effect of N shortage on SOM decomposition, the improvements related to the production and consumption of gases and an adequate simulations of gas transport in soil. On these bases, the assessment of trends and gaps in the modelling approaches currently employed to represent biogeochemical cycles in crop and grassland systems appears an essential step for future research.
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Affiliation(s)
- Lorenzo Brilli
- Università degli Studi di Firenze, Department of Agri-Food Production and Environmental Sciences, 50144 Florence, Italy; IBIMET-CNR, Via Caproni 8, 50145 Firenze, Italy.
| | - Luca Bechini
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences, Milan, Italy
| | - Marco Bindi
- Università degli Studi di Firenze, Department of Agri-Food Production and Environmental Sciences, 50144 Florence, Italy
| | - Marco Carozzi
- INRA, AgroParisTech, UMR1402 EcoSys, 78850 Thiverval-Grignon, France
| | - Daniele Cavalli
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences, Milan, Italy
| | - Richard Conant
- NREL, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Luca Doro
- Desertification Research Centre, Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy; Texas A&M AgriLife Research, Blackland Research & Extension Center, Temple, (TX), USA
| | | | - Roberta Farina
- CREA-RPS, Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Roma, Italy
| | - Roberto Ferrise
- Università degli Studi di Firenze, Department of Agri-Food Production and Environmental Sciences, 50144 Florence, Italy
| | - Nuala Fitton
- Institute of Biological and Environmental Sciences, University of Aberdeen, St Machar Drive, AB24 3UU Aberdeen, UK
| | - Rosa Francaviglia
- CREA-RPS, Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Roma, Italy
| | - Peter Grace
- Queensland University of Technology, Brisbane, Australia
| | - Ileana Iocola
- Desertification Research Centre, Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy
| | | | - Joël Léonard
- INRA, UR 1158 AgroImpact, site de Laon, F-02000 Barenton-Bugny, France
| | | | | | | | - Giovanna Seddaiu
- Desertification Research Centre, Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Joanna Sharp
- New Zealand Institute for Plant and Food Research, 7608 Lincoln, New Zealand
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, St Machar Drive, AB24 3UU Aberdeen, UK
| | - Ward N Smith
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
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Lawrence NC, Hauvermale AL, Dhingra A, Burke IC. Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest. Ecol Evol 2017; 7:8316-8328. [PMID: 29075451 PMCID: PMC5648657 DOI: 10.1002/ece3.3386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 11/06/2022] Open
Abstract
Bromus tectorum L. is an invasive winter annual grass naturalized across the United States. Numerous studies have investigated B. tectorum population structure and genetics in the context of B. tectorum as an ecological invader of natural areas and rangeland. Despite the wealth of information regarding B. tectorum, previous studies have not focused on, or made comparisons to, B. tectorum as it persists in individual agroecosystems. The objectives of this study were to assess the genetic diversity and structure, the occurrence of generalist and specialist genotypes, and the influence of climate on distribution of B. tectorum sourced exclusively from within small grain production regions of the Pacific Northwest. Genetic diversity of B. tectorum sourced from agronomic fields was found to be similar to what has been observed from other land use histories. Six distinct genetic clusters of B. tectorum were identified, with no evidence to indicate that any of the genetic clusters were better adapted to a particular geographical area or climate within the region. Given the apparent random spatial distribution of B. tectorum genetic clusters at the spatial scale of this analysis, unique genotypes may be well mixed within region, similar to what was reported for other inbreeding weedy grass species.
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Affiliation(s)
- Nevin C. Lawrence
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
- University of Nebraska‐LincolnScottsbluffNEUSA
| | | | - Amit Dhingra
- Department of HorticultureWashington State UniversityPullmanWAUSA
| | - Ian C. Burke
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
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47
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Sikkink KL, Kobiela ME, Snell-Rood EC. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. BMC Genomics 2017; 18:412. [PMID: 28549454 PMCID: PMC5446745 DOI: 10.1186/s12864-017-3787-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/30/2022] Open
Abstract
Background Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades. Results First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population. Conclusions Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristin L Sikkink
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA.
| | - Megan E Kobiela
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
| | - Emilie C Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
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48
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Gao F, Zou W, Xie L, Zhan J. Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan. Evol Appl 2017; 10:379-390. [PMID: 28352297 PMCID: PMC5367074 DOI: 10.1111/eva.12459] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/10/2017] [Indexed: 12/22/2022] Open
Abstract
Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade-specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.
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Affiliation(s)
- Fangluan Gao
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wenchao Zou
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lianhui Xie
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
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Global urban signatures of phenotypic change in animal and plant populations. Proc Natl Acad Sci U S A 2017; 114:8951-8956. [PMID: 28049817 DOI: 10.1073/pnas.1606034114] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Humans challenge the phenotypic, genetic, and cultural makeup of species by affecting the fitness landscapes on which they evolve. Recent studies show that cities might play a major role in contemporary evolution by accelerating phenotypic changes in wildlife, including animals, plants, fungi, and other organisms. Many studies of ecoevolutionary change have focused on anthropogenic drivers, but none of these studies has specifically examined the role that urbanization plays in ecoevolution or explicitly examined its mechanisms. This paper presents evidence on the mechanisms linking urban development patterns to rapid evolutionary changes for species that play important functional roles in communities and ecosystems. Through a metaanalysis of experimental and observational studies reporting more than 1,600 phenotypic changes in species across multiple regions, we ask whether we can discriminate an urban signature of phenotypic change beyond the established natural baselines and other anthropogenic signals. We then assess the relative impact of five types of urban disturbances including habitat modifications, biotic interactions, habitat heterogeneity, novel disturbances, and social interactions. Our study shows a clear urban signal; rates of phenotypic change are greater in urbanizing systems compared with natural and nonurban anthropogenic systems. By explicitly linking urban development to traits that affect ecosystem function, we can map potential ecoevolutionary implications of emerging patterns of urban agglomerations and uncover insights for maintaining key ecosystem functions upon which the sustainability of human well-being depends.
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50
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The Eco-Evolutionary Imperative: Revisiting Weed Management in the Midst of an Herbicide Resistance Crisis. SUSTAINABILITY 2016. [DOI: 10.3390/su8121297] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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