- Email: [email protected]
A computer vision for rice disease identification to support Integrated Pest Management
Abstracts / Crop Protection 61 (2014) 102–110
3. Much of the pest-induced crop losses are due to the extensive adoption of monocultures and it is recommended to promote higher levels of crop biodiversity. 4. The resurgence of the brown planthopper, Nilaparvata lugens, in Asian rice is primarily due to the indiscriminate use of insecticides and the subsequent destruction of the pests’ natural enemies 5. Invasive species have a major impact on natural terrestrial and agricultural systems; Invasive plants in natural systems and invasive arthropods in major agricultural systems. 6. Tactics that preserve biodiversity are a major component in IPM strategies. 7. As spiders play a major role as predators in both natural and agricultural ecosystems quantitative studies on spider biodiversity are needed to understand the impact of climate change. 8. In Indonesia the environmental and health benefits derived from the employment of biological control agents have resulted in increased profits to farmers as consumers are willing to pay more for pesticide-free food. 9. To manage the invasive pest, the cassava mealybug, Phenacoccus manihoti, the parasitoid, Anagyrus lopezi, has been introduced into Thailand from Benin, West Africa where it is an effective biological control agent. 10. Classical biological control is used to manage invasive plants in natural systems and conservation biological control employed to manage invasive arthropods in agricultural systems. 11. Rouging has been effective in managing tospoviruses in tropical tomatoes. 12. There is a need to develop management strategies for virus diseases in tropical vegetable crops because no effective and biologically safe insecticides have been identified. This conference has provided an understanding of role of invasive species in the terrestrial natural and agricultural biodiversity and their management as well as the need for implementation of various safe and efficient crop protection technologies for preservation of biodiversity. Promoting biodiversity by the incorporation of diverse crop germplasm, resistant varieties, biological control agents, use of biopesticides and pheromones, and other technologies as components in an IPM package for each crop was recommended. This strategy, which preserves and increases biodiversity, has been shown to effectively manage pests and promote stability in agricultural production systems.
E-mail addresses: [email protected] (P. Director), [email protected] (E.A. Heinrichs)
103
Figure 2. Dr. Guru Ghosh, Vice President for Outreach and International Affairs, Virginia Tech, Blacksburg, VA, USA welcoming a global assemblage of participants to the Biodiversity and IPM conference.
Figure 3. Dr. Dan Sembel, North Sulawesi IPM Innovation Lab coordinator explaining IPM components implemented in a strawberry field near Manado, Indonesia during the Biodiversity and IPM Conference field trip.
A COMPUTER VISION FOR RICE DISEASE IDENTIFICATION TO SUPPORT INTEGRATED PEST MANAGEMENT Auzi Asfarian 1, *, Yeni Herdiyeni 1, Aunu Rauf 2, Kikin Hamzah Mutaqin 2. 1 Computer Science Department, Bogor Agricultural University, Dramaga, Bogor 16680, Indonesia; 2 Plant Protection Department, Bogor Agricultural University, Dramaga, Bogor 16680, Indonesia
Figure 1. Wallace in the Malay Archipelago. A painting by Evstafieff in the collection of Down House. ÓEnglish Heritage Photo Library.
Rice is the main source of carbohydrates consumed by the Indonesian population. According to Badan Pusat Statistik, the average amount per capita rice consumption reached 113.5 kilograms in 2011. On the other hand, the population of Indonesia, which showed an increasing trend over the last decade, demands increased national rice production. In addition to quantity, the quality of rice, which is the most important factor in the consumption of rice, must be maintained. One way to achieve this is to manage rice diseases. In using the Integrated Pest Management (IPM) approach, the first step is to properly diagnose the rice diseases so that the correct treatments can be taken up as soon as possible. However, in certain regions, experts may not be available to correctly identify the diseases. Computer vision can effectively solve this problem by rapidly identifying rice diseases through the employment of image processing techniques. We propose a new method of texture analysis to identify rice diseases using fractal fourier. In our study we used the images of four rice diseases: bacterial leaf blight (Xanthomonas oryzae), blast (Pyricularia oryzae), brown spot (Helminthosporium sp.) and tungro virus. The image of the rice leaf is converted to CIELab color space. The disease spots are
104
Abstracts / Crop Protection 61 (2014) 102–110
then segmented using Otsu's threshold on ‘a’ component. The fractal descriptor of each spot is then estimated by using Fourier spectrum on ‘L’ component. The descriptor is then used to identify the disease using the probabilistic neural network. This method is able to achieve a 92.5% of accuracy. The experimental results showed that the proposed method is a promising technique to support IPM by the rapid identification of rice diseases. * Corresponding author. E-mail address: [email protected] (A. Asfarian)
BEGOMOVIRUS DIVERSITY, PHYLOGEOGRAPHY, AND POPULATION GENETICS IN CULTIVATED AND UNCULTIVATED PLANT ECOSYSTEMS IN PAKISTAN J.K. Brown 1, *, H.-W. Herrmann 1, M. Zia-Ur-Rehman 1,2, U. Hameed 1, 2, M.S. Haider 1, 2. 1 School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; 2 Institute of Agricultural Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan Recent biodiversity research suggests that biodiversity may control, rather than respond to, our planets biophysical processes and thus is directly related to ecosystem functioning. Biodiversity encompasses many different levels, ranging from taxonomic dimensions (species richness) to functional diversity. To study these multiple dimensions is challenging and requires exploration of symbioses among organisms, and relationships with respect to complexity owing to multitrophic symbioses. Such approaches are necessary to make possible the extrapolation of these findings to predictions of ecosystem-wide consequences, at the interface of plant virus communities associated with endemic, genetically diverse, and more sparsely distributed plants, compared to agriculturally selected, genetically homogeneous, monoculture scenarios. To pursue this range of questions we are employing as the study system the plant virus genus, Begomovirus (Geminiviridae), a super-abundant group of viruses undergoing an as yet largely unknown extent of population expansion, and their whitefly vector Bemisia tabaci (Genn.) sibling species group, a (cryptic) complex of poorly studied genetic variants that exhibit a range of phenotypes and varying degrees of genetic isolation. Our goal is to identify dimensions of virus and/or begomoviral-associated satellite diversity/diversification and related ecosystem patterns (host, vector, spatial, time, etc.), ultimately to make possible the prediction of consequences around which mitigation efforts to promote biodiversity and thereby an increase overall biomass production, could be devised. Begomoviruses are ssDNA viruses, are widely distributed in endemic/ruderal plant species, and cause diseases in cultivated species in which they have emerged as pathogens during the past half century (with the expansion of monoculture crop production). The concomitant upsurgence and/or trans-continental introduction of agro-ecosystem adapted B. tabaci vector haplotypes with greater fitness (compared to most other haplotypes) have been shown to greatly influence virus diversification. Plant virus diversity has largely been studied at the species or family levels, on large geographical scales, or based on virus-satellite richness within diverse host plants. Diversity studies of begomoviruses addressing within viral species genetic structure, and its relation to geographic distance or potential gene flow barriers, and/or to the health of the larger community in relation to biomass production, remain largely unstudied. Here we evaluated begomoviral-satellite sequence diversity in crop and ruderal plant species, in proximity to a cotton-vegetable agroecosystem. Viral genome-beta satellite datasets were obtained and analyzed with respect to phylogeography and demographic changes over time. Genetic diversity and gene flow analysis employs F statistics and Bayesian clustering. Additionally, results using RCA and PCR approaches have been compared with those revealed by the NGS platform Illumina HiSeq 2000 for the same sample sets to estimate diversity. * Corresponding author. E-mail address: [email protected] (J.K. Brown)
SUSTAINABLE YIELD: THE CONTRIBUTION OF MODERN BREEDING AND BIOTECHNOLOGY IN HELPING FARMERS INCREASE YIELD AND REDUCE ENVIRONMENTAL IMPACTS IN ASIA Harvey Glick 1, 2, *. 1 Regulatory Policy and Scientific Affairs, USA; 2 Monsanto Company, USA
Increasing food productivity is a primary societal challenge and technologies to increase yield remain of paramount importance. The yield gains from the Green Revolution of the previous century have plateaued and new yield technologies are urgently needed. Increasingly, there is a demand for these new yield technologies to contribute to a reduced environmental footprint for agriculture with focus on improving the efficiency of resource utilization (less water, energy, pesticides, fertilizers, etc). This additional constraint of sustainability is critically important but it increases the difficulty and cost of developing new yield technologies. In addition to the discovery and development of new innovative sustainable yield technologies is the need for innovative government policies to facilitate the transfer of these technologies from lab to farm. Recent advances in modern breeding and biotechnology have delivered improved seeds with a variety of improved agronomic traits that have resulted in significant productivity increases. Herbicide tolerant crops and crops with protection against insect and virus pests are providing yield increases of 5-50% for farmers in both developed and developing countries. Crops with tolerance to drought are now becoming available to farmers and crops with tolerance to salinity, flooding, infertility and a range of abiotic stresses are now under development. These new crops will help further protect and improve yields under suboptimal growing conditions that may be accelerated by increasingly variable climatic conditions. Equally important, over the past 15 years, new high yield crops from advanced breeding have significantly reduced the amount of land, water, energy, and pesticides required to produce corn and soybeans. This has been demonstrated in both large, highly mechanized farms in North America and small, less technified farms in the Philippines. In the Philippines, the significant productivity gains attributed to planting new high yielding hybrid corn from modern breeding has underscored the positive return on investment from national policies supporting research and development in these new agricultural technologies. These significant achievements have come from the integration of these new high yielding seeds from modern breeding with local best management production practices. These achievements contribute to improved farmer profitability, they contribute to a reduction in inputs per unit of crop harvested and they help address the growing societal demand for food produced in a more sustainable production system. National policies and regulations have lagged behind these innovative scientific developments and the transfer of these new high yielding crops from the laboratory to the farmer has been slow in Asia. Local research and development of important, indigenous crops has been impacted by the difficulty and cost in bringing these new crops to the market. This has significantly delayed efforts to address productivity shortfalls and reduce the footprint of agriculture and food security in many countries of Asia. * Corresponding author. E-mail address: [email protected] (H. Glick)
APHIDS–SUPER-PESTS IN ANNUAL CROPPING SYSTEMS: WHAT DEFINES THEIR DIVERSITY, DRIVES THEIR PEST STATUS, AND MITIGATES THEIR ECONOMIC CONSEQUENCES? Michael E. Irwin Professor Emeritus *. University of Illinois, UrbanaChampaign, University of Arizona, Tucson, USA Biological diversity (i.e., biodiversity) is a concept that, on the one hand, is frequently linked with natural environments such as wildlife refuges and other conserved natural landscapes and refers to the numbers and assortments of taxa they encompass. Genetic diversity, on the other hand, defines another aspect of biodiversity and can be thought of in terms of cultivars, isolines, varieties, and variants of a given species or closely related species. This paper addresses yet another aspect of diversity by exploring aphids (Homoptera: Aphididae) in annual cropping systems. It examines their multiple roles as crop pests and as vectors of plant pathogens, it reviews their diversity and suggests concepts through which aphids can be managed within and among agroecosystems. Aphids form a remarkable assemblage of species and abound in most annual cropping systems, especially those grown in temperate, arid, and subtropical environments. They fly, often over very long distances, and enter an agricultural field by the multitudes. In fact, countless tens-ofmillions of specimens comprising 30-80 aphid species can alight in a single
3. Much of the pest-induced crop losses are due to the extensive adoption of monocultures and it is recommended to promote higher levels of crop biodiversity. 4. The resurgence of the brown planthopper, Nilaparvata lugens, in Asian rice is primarily due to the indiscriminate use of insecticides and the subsequent destruction of the pests’ natural enemies 5. Invasive species have a major impact on natural terrestrial and agricultural systems; Invasive plants in natural systems and invasive arthropods in major agricultural systems. 6. Tactics that preserve biodiversity are a major component in IPM strategies. 7. As spiders play a major role as predators in both natural and agricultural ecosystems quantitative studies on spider biodiversity are needed to understand the impact of climate change. 8. In Indonesia the environmental and health benefits derived from the employment of biological control agents have resulted in increased profits to farmers as consumers are willing to pay more for pesticide-free food. 9. To manage the invasive pest, the cassava mealybug, Phenacoccus manihoti, the parasitoid, Anagyrus lopezi, has been introduced into Thailand from Benin, West Africa where it is an effective biological control agent. 10. Classical biological control is used to manage invasive plants in natural systems and conservation biological control employed to manage invasive arthropods in agricultural systems. 11. Rouging has been effective in managing tospoviruses in tropical tomatoes. 12. There is a need to develop management strategies for virus diseases in tropical vegetable crops because no effective and biologically safe insecticides have been identified. This conference has provided an understanding of role of invasive species in the terrestrial natural and agricultural biodiversity and their management as well as the need for implementation of various safe and efficient crop protection technologies for preservation of biodiversity. Promoting biodiversity by the incorporation of diverse crop germplasm, resistant varieties, biological control agents, use of biopesticides and pheromones, and other technologies as components in an IPM package for each crop was recommended. This strategy, which preserves and increases biodiversity, has been shown to effectively manage pests and promote stability in agricultural production systems.
E-mail addresses: [email protected] (P. Director), [email protected] (E.A. Heinrichs)
103
Figure 2. Dr. Guru Ghosh, Vice President for Outreach and International Affairs, Virginia Tech, Blacksburg, VA, USA welcoming a global assemblage of participants to the Biodiversity and IPM conference.
Figure 3. Dr. Dan Sembel, North Sulawesi IPM Innovation Lab coordinator explaining IPM components implemented in a strawberry field near Manado, Indonesia during the Biodiversity and IPM Conference field trip.
A COMPUTER VISION FOR RICE DISEASE IDENTIFICATION TO SUPPORT INTEGRATED PEST MANAGEMENT Auzi Asfarian 1, *, Yeni Herdiyeni 1, Aunu Rauf 2, Kikin Hamzah Mutaqin 2. 1 Computer Science Department, Bogor Agricultural University, Dramaga, Bogor 16680, Indonesia; 2 Plant Protection Department, Bogor Agricultural University, Dramaga, Bogor 16680, Indonesia
Figure 1. Wallace in the Malay Archipelago. A painting by Evstafieff in the collection of Down House. ÓEnglish Heritage Photo Library.
Rice is the main source of carbohydrates consumed by the Indonesian population. According to Badan Pusat Statistik, the average amount per capita rice consumption reached 113.5 kilograms in 2011. On the other hand, the population of Indonesia, which showed an increasing trend over the last decade, demands increased national rice production. In addition to quantity, the quality of rice, which is the most important factor in the consumption of rice, must be maintained. One way to achieve this is to manage rice diseases. In using the Integrated Pest Management (IPM) approach, the first step is to properly diagnose the rice diseases so that the correct treatments can be taken up as soon as possible. However, in certain regions, experts may not be available to correctly identify the diseases. Computer vision can effectively solve this problem by rapidly identifying rice diseases through the employment of image processing techniques. We propose a new method of texture analysis to identify rice diseases using fractal fourier. In our study we used the images of four rice diseases: bacterial leaf blight (Xanthomonas oryzae), blast (Pyricularia oryzae), brown spot (Helminthosporium sp.) and tungro virus. The image of the rice leaf is converted to CIELab color space. The disease spots are
104
Abstracts / Crop Protection 61 (2014) 102–110
then segmented using Otsu's threshold on ‘a’ component. The fractal descriptor of each spot is then estimated by using Fourier spectrum on ‘L’ component. The descriptor is then used to identify the disease using the probabilistic neural network. This method is able to achieve a 92.5% of accuracy. The experimental results showed that the proposed method is a promising technique to support IPM by the rapid identification of rice diseases. * Corresponding author. E-mail address: [email protected] (A. Asfarian)
BEGOMOVIRUS DIVERSITY, PHYLOGEOGRAPHY, AND POPULATION GENETICS IN CULTIVATED AND UNCULTIVATED PLANT ECOSYSTEMS IN PAKISTAN J.K. Brown 1, *, H.-W. Herrmann 1, M. Zia-Ur-Rehman 1,2, U. Hameed 1, 2, M.S. Haider 1, 2. 1 School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; 2 Institute of Agricultural Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan Recent biodiversity research suggests that biodiversity may control, rather than respond to, our planets biophysical processes and thus is directly related to ecosystem functioning. Biodiversity encompasses many different levels, ranging from taxonomic dimensions (species richness) to functional diversity. To study these multiple dimensions is challenging and requires exploration of symbioses among organisms, and relationships with respect to complexity owing to multitrophic symbioses. Such approaches are necessary to make possible the extrapolation of these findings to predictions of ecosystem-wide consequences, at the interface of plant virus communities associated with endemic, genetically diverse, and more sparsely distributed plants, compared to agriculturally selected, genetically homogeneous, monoculture scenarios. To pursue this range of questions we are employing as the study system the plant virus genus, Begomovirus (Geminiviridae), a super-abundant group of viruses undergoing an as yet largely unknown extent of population expansion, and their whitefly vector Bemisia tabaci (Genn.) sibling species group, a (cryptic) complex of poorly studied genetic variants that exhibit a range of phenotypes and varying degrees of genetic isolation. Our goal is to identify dimensions of virus and/or begomoviral-associated satellite diversity/diversification and related ecosystem patterns (host, vector, spatial, time, etc.), ultimately to make possible the prediction of consequences around which mitigation efforts to promote biodiversity and thereby an increase overall biomass production, could be devised. Begomoviruses are ssDNA viruses, are widely distributed in endemic/ruderal plant species, and cause diseases in cultivated species in which they have emerged as pathogens during the past half century (with the expansion of monoculture crop production). The concomitant upsurgence and/or trans-continental introduction of agro-ecosystem adapted B. tabaci vector haplotypes with greater fitness (compared to most other haplotypes) have been shown to greatly influence virus diversification. Plant virus diversity has largely been studied at the species or family levels, on large geographical scales, or based on virus-satellite richness within diverse host plants. Diversity studies of begomoviruses addressing within viral species genetic structure, and its relation to geographic distance or potential gene flow barriers, and/or to the health of the larger community in relation to biomass production, remain largely unstudied. Here we evaluated begomoviral-satellite sequence diversity in crop and ruderal plant species, in proximity to a cotton-vegetable agroecosystem. Viral genome-beta satellite datasets were obtained and analyzed with respect to phylogeography and demographic changes over time. Genetic diversity and gene flow analysis employs F statistics and Bayesian clustering. Additionally, results using RCA and PCR approaches have been compared with those revealed by the NGS platform Illumina HiSeq 2000 for the same sample sets to estimate diversity. * Corresponding author. E-mail address: [email protected] (J.K. Brown)
SUSTAINABLE YIELD: THE CONTRIBUTION OF MODERN BREEDING AND BIOTECHNOLOGY IN HELPING FARMERS INCREASE YIELD AND REDUCE ENVIRONMENTAL IMPACTS IN ASIA Harvey Glick 1, 2, *. 1 Regulatory Policy and Scientific Affairs, USA; 2 Monsanto Company, USA
Increasing food productivity is a primary societal challenge and technologies to increase yield remain of paramount importance. The yield gains from the Green Revolution of the previous century have plateaued and new yield technologies are urgently needed. Increasingly, there is a demand for these new yield technologies to contribute to a reduced environmental footprint for agriculture with focus on improving the efficiency of resource utilization (less water, energy, pesticides, fertilizers, etc). This additional constraint of sustainability is critically important but it increases the difficulty and cost of developing new yield technologies. In addition to the discovery and development of new innovative sustainable yield technologies is the need for innovative government policies to facilitate the transfer of these technologies from lab to farm. Recent advances in modern breeding and biotechnology have delivered improved seeds with a variety of improved agronomic traits that have resulted in significant productivity increases. Herbicide tolerant crops and crops with protection against insect and virus pests are providing yield increases of 5-50% for farmers in both developed and developing countries. Crops with tolerance to drought are now becoming available to farmers and crops with tolerance to salinity, flooding, infertility and a range of abiotic stresses are now under development. These new crops will help further protect and improve yields under suboptimal growing conditions that may be accelerated by increasingly variable climatic conditions. Equally important, over the past 15 years, new high yield crops from advanced breeding have significantly reduced the amount of land, water, energy, and pesticides required to produce corn and soybeans. This has been demonstrated in both large, highly mechanized farms in North America and small, less technified farms in the Philippines. In the Philippines, the significant productivity gains attributed to planting new high yielding hybrid corn from modern breeding has underscored the positive return on investment from national policies supporting research and development in these new agricultural technologies. These significant achievements have come from the integration of these new high yielding seeds from modern breeding with local best management production practices. These achievements contribute to improved farmer profitability, they contribute to a reduction in inputs per unit of crop harvested and they help address the growing societal demand for food produced in a more sustainable production system. National policies and regulations have lagged behind these innovative scientific developments and the transfer of these new high yielding crops from the laboratory to the farmer has been slow in Asia. Local research and development of important, indigenous crops has been impacted by the difficulty and cost in bringing these new crops to the market. This has significantly delayed efforts to address productivity shortfalls and reduce the footprint of agriculture and food security in many countries of Asia. * Corresponding author. E-mail address: [email protected] (H. Glick)
APHIDS–SUPER-PESTS IN ANNUAL CROPPING SYSTEMS: WHAT DEFINES THEIR DIVERSITY, DRIVES THEIR PEST STATUS, AND MITIGATES THEIR ECONOMIC CONSEQUENCES? Michael E. Irwin Professor Emeritus *. University of Illinois, UrbanaChampaign, University of Arizona, Tucson, USA Biological diversity (i.e., biodiversity) is a concept that, on the one hand, is frequently linked with natural environments such as wildlife refuges and other conserved natural landscapes and refers to the numbers and assortments of taxa they encompass. Genetic diversity, on the other hand, defines another aspect of biodiversity and can be thought of in terms of cultivars, isolines, varieties, and variants of a given species or closely related species. This paper addresses yet another aspect of diversity by exploring aphids (Homoptera: Aphididae) in annual cropping systems. It examines their multiple roles as crop pests and as vectors of plant pathogens, it reviews their diversity and suggests concepts through which aphids can be managed within and among agroecosystems. Aphids form a remarkable assemblage of species and abound in most annual cropping systems, especially those grown in temperate, arid, and subtropical environments. They fly, often over very long distances, and enter an agricultural field by the multitudes. In fact, countless tens-ofmillions of specimens comprising 30-80 aphid species can alight in a single