Omics-driven strategies for integrated insect-pest and disease management
DOI:
https://doi.org/10.58628/JAE-2622-101Keywords:
Omics technologies, Integrated insect-pest and disease management (IPDM), Sustainable agriculture, RNA interference (RNAi), Biopesticides and microbial consortia, Climate-smart agricultureAbstract
Agriculture is increasingly challenged by insect-pests and diseases that threaten global food security, farmer livelihoods, and ecosystem stability. Conventional management strategies, particularly chemical pesticides, have offered short-term solutions but are constrained for resistance development, environmental contamination, and health concerns. This has created an urgent need for innovative, sustainable, and knowledge-driven approaches to crop protection. In this context, omics technologies, including genomics, transcriptomics, proteomics, metabolomics, biopesticides, microbial consortia and microbiomics, have emerged as transformative tools for integrated insect-pest and disease management (IPDM). Omics approaches offer a comprehensive understanding of biological systems by deciphering host-pathogen-pest interactions. Genomics enables the identification of resistance genes and virulence factors, while transcriptomics reveals dynamic gene expression during stress or infection. Proteomics and metabolomics uncover functional proteins and metabolites involved in defense responses, offering insights into biochemical pathways for crop protection. Microbiomics highlights the role of beneficial microbes in enhancing plant immunity and suppressing pests, opening avenues for bio-based interventions. Integration of omics data supports eco-friendly strategies such as molecular diagnostics for early detection, RNA interference (RNAi)-based pest control, and marker-assisted breeding for resistant varieties. Furthermore, omics-driven insights facilitate the development of biopesticides and microbial consortia that complement traditional IPM practices. Beyond pest control, omics contributes to reducing chemical dependency, enhancing biodiversity, improving soil and water health, empowering farmers with knowledge, and advancing climate-smart agriculture. Thus, omics technologies represent a paradigm shift in insect-pest and disease management, enabling a transition from reactive, pesticide-dependent practices to proactive, knowledge-intensive solutions. Their integration into IPDM frameworks promises resilient crops, reduced ecological footprints, and sustainable food security for future generations.
References
Abdullah RR. 2019. Insecticidal activity of secondary metabolites of locally isolated fungal strains against some cotton insect pests. Journal of plant protection and pathology. 10 (12): 647-653.
Adeleke BS, Babalola OO. 2022. Meta-omics of endophytic microbes in agricultural biotechnology. Biocatal Agric Biotechnol. 42:102332.
Ahmad I, del Mar Jimenez-Gasco M, Luthe DS, Shakeel SN and Barbercheck ME. 2020. Endophytic Metarhizium robertsii promotes maize growth, suppresses insect growth, and alters plant defense gene expression. Biological control. 144: 104167.
Allwood JW, Clarke A, Goodacre R, Mur LA. 2010. Dual metabolomics: a novel approach to understanding plant–pathogen interactions. Phytochemistry. 71(5–6): 590–7.
Angelella GM, Holland JD & Kaplan I. 2016. Landscape composition is more important than local management for crop virus–insect vector interactions. Agric. Ecosyst. Environ., 233: 253-261.
Arbona V & Gomez-Cadenas A. 2016. Metabolomics of disease resistance in crops. Curr Issues Mol Biol. 19: 13–30.
Askew WT, Edwards MG, Gatehouse AM.(2024). Ex vivo delivery of dsRNA targeting ryanodine receptors for control of Tuta absoluta. Pest Manag. Sci. , 80, 6400–6408.
Ayilara MS, Adeleke BS, Akinola SA, Fayose CA, Adeyemi UT, Gbadegesin LA, et al. 2023. Biopesticides as a promising alternative to synthetic pesticides: A case for microbial pesticides, phytopesticides, and nanobiopesticides. Frontiers in Microbiology, 14:1040901. DOI: 10.3389/fmicb.2023.1040901
Azevedo JL. 1998. Endophytic microorganisms. In: Ecologia Microbiana. Embrapa Meio Ambiente, Jaguariúna, Brazil, pp. 117–137.
Balotf S, Tegg RS, Nichols DS, Wilson CR. 2021. Spore germination of the obligate biotroph Spongospora subterranea: transcrip¬tome analysis reveals germination associated genes. Front Microbiol. ;12: 691877.
Batz P, Will T, Thiel S, Ziesche T M, and Joachim C. 2023. From identification to forecasting: the potential of image recognition and artificial intelligence for aphid pest monitoring. Front. Plant Sci. 14:1150748. doi: 10.3389/fpls.2023.1150748.
Bhagat J, Kaur A, Yadav AK, Sharma V, and Chadha BS. 2016. Cholinesterase inhibitor (altenuene) from an endophytic fungus Alternaria alternata: optimization, purification and characterization. Journal of Applied Microbiology. 121(4): 1015–1025.
Bhatia A, Chug A, and Singh AP. 2020. “Hybrid SVM-LR classifier for powdery mildew disease prediction in tomato plant”, in Proceedings of the 2020 7th International Conference on Signal Processing and Integrated Networks (SPIN), (Noida, India), 218–223.
Bock CH, Poole GH, Parker PE, Gottwald TR. 2010. Plant disease severity estimated visually, by digital photography and image analysis, and by hyperspectral imaging. Crit Rev Plant Sci.; 29 (2): 59–107. ttps://doi.org/10.1080/07352681003617285.
Bourhis Y, Bell J R, van den Bosch F, and Milne A E. 2021. Artificial neural networks for monitoring network optimisation—a practical example using a national insect survey. Environ. Model. Softw. 135:104925. doi: 10.1016/j.envsoft.2020.104925.
Brosset A, Blande JD. 2022. Volatile-mediated plant–plant interactions: volatile organic compounds as modulators of receiver plant defence, growth, and reproduction. J Exp Bot. 73(2):511–528.
Carvalho CR, Ferreira-D'Silva A, Wedge DE, Cantrell CL, and Rosa LH. 2018. Antifungal activities of cytochalasins produced by Diaporthe miriciae, an endophytic fungus associated with tropical medicinal plants. Canadian Journal of Microbiology. 64(11): 835–843.
Cervantes-Perez SA, Zogli P, Amini S, et al. 2024. Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process. Plant Commun. https://doi.org/10.1016/j.xplc.2024.100984.
Chaerle L, Hagenbeek D, De Bruyne E, Valcke R, Van Der Straeten D. 2004. Thermal and chlorophyll-fluorescence imaging distinguishes plant-pathogen interactions at an early stage. Plant Cell Physiol. 45(7): 887–96. https://doi.org/10.1093/pcp/pch097.
Chao H, Zhang S, Hu Y, Ni Q, Xin S, Zhao L, Ivanisenko VA, Orlov YL & Chen M. 2023. Integrating omics databases for enhanced crop breeding. J Integr Bioinf. 20.
Chao H, Zhang S, Hu Y, Ni Q, Xin S, Zhao L.et al. 2024. Integrating omics databases for enhanced crop breeding. J. Integr. Bioinform. 20:12. 10.1515/jib-2023-0012.
Chen JZ, Jiang YX, Li MW, Li JW, Zha BH, Yang G. 2021. Double-stranded RNA-degrading enzymes reduce the efficiency of RNA interference in Plutella xylostella. Insects 12, 712.
Christakakis P, Papadopoulou G, Mikos G, Kalogiannidis N, Ioannidis D, Tzovaras, D., et al. 2024. Smartphone-based citizen science tool for plant disease and insect Pest detection using artificial intelligence. Technologies 12:101. doi: 10.3390/technologies12070101.
Colarusso AV, Goodchild-Michelman I, Rayle M, Zomorrodi AR. 2021. Computational modeling of metabolism in microbial communities on a genome-scale. Current Opinion in Systems Biology, 26: 46-57.
Contreras-Cornejo HA, Schmoll M, Esquivel-Ayala BA, Gonzalez-Esquivel CE, Rocha-Ramírez V & Larsen J. et al. 2024. Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems. Microbiol. Res. 281:127621.
Darif N, Vogelsang K, Vorgia E, Schneider D, Deligianni E, Geibel S, Vontas J, Denecke S. 2023. Cell penetrating peptides are versatile tools for enhancing multimodal uptake into cells from pest insects. Pestic. Biochem. Physiol. 190, 105317.
Diab MK, Mead HM, Khedr MA, Nafie MS, Abu-Elsaoud A.M, Hanora A and El-Shatoury SA. 2023. Endophytic actinobacteria from wild medicinal plants are a natural source of insecticide to control the African cotton leafworm (Spodoptera littoralis). Applied microbiology and biotechnology express. 13 (1): 47.
Dimkic I, Janakiev T, Petrović M, Degrassi G, Fira D 2022 Plant-associated Bacillus and Pseudomonas antimicrobial activities in plant disease suppression via biological control mechanisms—a review. Physiol Mol Plant Pathol. 117:101754.
Dong Y, Xia X, Ahmad D, Wang Y, Zhang X, Wu L, He Y. 2023. Investigating the resistance mechanism of wheat varieties to Fusarium head blight using comparative metabolomics. Int J Mol Sci. 24(4): 3214.
Doni F, Miranti M, Mispan MS, Mohamed Z & Uphoff N. 2022. Multi-omics approaches for deciphering the microbial modulation of plants’ genetic potentials: what’s known and what’s next? Rhizosphere, 24:100613. https://doi.org/10.1016/j.rhisph.2022.100613
Duchene O, Vian JF & Celette FF. 2017. Intercropping with legume for agroecological cropping systems: complementarity and facilitation processes and the importance of soil microorganisms. A review. Agric. Ecosyst. Environ., 240: 148-161.
Elston KM, Maeda GP, Perreau J, Barrick J. (2013). Addressing the challenges of symbiont-mediated RNAi in aphids. PeerJ 2023, 11, e14961.
Ercoli MF, Luu DD, Rim EY, Shigenaga A, Teixeira de Araujo A Jr, Chern M, Jain R, Ruan R, Joe A, Stewart V, Ronald P. 2022. Plant immunity: rice XA21-mediated resistance to bacterial infection. Proc Natl Acad Sci USA.; 119(8): e2121568119.
Eshel G, Araus V, Undurraga S, et al. 2021. Plant ecological genomics at the limits of life in the Atacama Desert. Proceedings of the National Academy of Sciences, USA, 118, e2101177118.
Evangelisti E, Rey T, and Schornack S. 2014. Cross interference of plant development and plant–microbe interactions. Current Opinion in Plant Biology. 20: 118–126. https://doi.org/10.1016/j.pbi.2014.05.014.
Fan Y, Song H, Abbas M, Wang Y, Liu X, Li T, Ma E, Zhu KY, Zhang J.(2022). The stability and sequence cleavage preference of dsRNA are key factors differentiating RNAi efficiency between migratory locust and Asian corn borer. Insect Biochem. Mol. Biol. 143, 103738.
FAO 2025. Guidance on integrated pest management for the world’s major crop pests.
Farrakh S, Khalid S, Rafique A, Riaz N, and Mujeeb-Kazi A. 2016. Identification of stripe rust resistant genes in resistant synthetic hexaploid wheat accessions using linked markers. Plant Genetic Resour. 14, 219–225. doi: 10.1017/ S1479262115000283.
Fernandez RG, Novo JVJ. 2011. Contribution of proteomics to the study of plant pathogenic fungi. J Proteome Res. 111: 3–16.
Filho EB, and Macedo LPM. 2011. Fundamentals of biological control of pest insects. IFRN Press, Natal, Brazil.
Flynt AS. (2021). Insecticidal RNA interference, thinking beyond long dsRNA. Pest Manag. Sci. 77, 2179–2187.
Fuentes M T, Lenardis A, and De la Fuente E B. (2018). Insect assemblies related to volatile signals emitted by different soybean–weeds–herbivory combinations. Agr. Ecosyst. Environ. 255, 20–26. doi: 10.1016/j.agee.2017.12.007.
Gao Y, Xu H, Shen Y, Wang J. 2013. Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-seq technique. Plant Mol Biol.; 81: 363–78.
Garciglia-Mercado C, Contreras CA, Choix FJ, de-Bashan LE, Gomez-Anduro GA & Palacios OA. 2024. Metabolic & physiological adaptations of microalgal growth-promoting bacterium Azospirillum brasilense growing under biogas atmosphere: A microarray-based transcriptome analysis. Arch Microbiol., 206:173. https://doi.org/10.1007/s00203-024-03890-z.
Govindarajan M, Balandreau J, Kwon S-W, Weon, H.-Y., and Lakshminarasimhan, C. 2008. Effects of inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice. Microbial Ecology. 55: 21–37.
Guerra-Guimaraes L, Tenente R, Pinheiro C, et al. 2015. Proteomic analysis of apoplastic fluid of Coffea arabica leaves highlights novel biomarkers for resistance against Hemileiavastatrix. Front Plant Sci.; 6: 478.
Gundel PE, Sun P, Charlton ND, Young CA, Miller TE, et al. 2020. Simulated folivory increases vertical transmission of fungal endophytes that deter herbivores and alter tolerance to herbivory in Poa autumnalis. Annals of Botany. 125(6): 981–991.
Gupta R, Lee SE, Agrawal GK, et al. 2015. Understanding the plant–pathogen interactions in the context of proteomics-generated apoplastic proteins inventory. Front Plant Sci. 6: 352.
Haas B, Kamoun S. Zody M, et al. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. ;461:393–98. https://doi.org/10.1104/pp.114.252213.
Haldhar SM, Bhargava R, Choudhary BR, Pal G and Kumar S. 2013. Allelochemical resistance traits of muskmelon (Cucumis melo) against the fruit fly (Bactrocera cucurbitae) in a hot arid region of India. Phytoparasitica, 41: 473-481.
Haldhar SM, Bhargava R, Krishna H, Berwal MK and Saroj PL. 2018a. Bottom-up effects of different host plant resistance cultivars on ber (Ziziphus mauritiana)- fruit fly (Carpomyia vesuviana) interactions. Crop Protection, 106: 117-124.
Haldhar SM, Bhargava R, Singh RS, Samadia DK, Jat GC and Singh D. 2019. Do bottom-up effects (resistance) of different accessions of Indian cherry (Cordia myxa L.) help against tingid bug [Dictyla cheriani (Drake)] attack? Journal of Agriculture and Ecology, 8: 84-103.
Haldhar SM, Kumar R, Corrado G, Berwal MK, Gora JS, Thaochan N, Samadia DK, Hussain T, Rouphael Y, Kumar P and Basile B. 2022. A field screening of a pomegranate (Punica granatum) ex-situ germplasm collection for resistance against the false spider mite (Tenuipalpus punicae). Agriculture, 12, 1686. https://doi.org/10.3390/agriculture12101686.
Haldhar SM, Samadia DK, Bhargava R, Choudhary BR and Singh D. 2018b. Host plant accessions determine bottom-up effect of snapmelon (Cucumis melo var. momordica) against melon fly (Bactrocera cucurbitae (Coquillett)). Breeding Science, 68: 499-507.
Haldhar SM, Singh AK, Gora JS, Berwal MK and Hussain T. 2023a. Plant-insect interactions in different genotypes of ber (Ziziphus mauritiana L) against fruit borer (Meridarchis scyrodes Meyrick). Journal of Agriculture and Ecology, 16: 78-87; https: //doi.org/10.58628/JAE-2316-216.
Haldhar SM, Singh AK, Kumar K and Sarolia DK. 2018c. Antixenotic and allelochemical resistance traits of ber (Ziziphus mauritiana) against stone weevil, Aubeus himalayanus in hot arid region of India. Indian Journal of Arid Horticulture, 13: 50-58.
Haldhar SM, Singh RS and Singh D. 2021. HPSI of date palm (Phoenix dactylifera L.) varieties/genotypes against fruit borers, Batrachedra amydraula and Arenipses sabella in hot arid region. Journal of Agriculture and Ecology, 11: 26-36.
Haldhar SM, Singh S, Singh AK, Bhargava R, Singh RS and Singh D. 2016. Host Plant Resistance (HPR) study in Jamun (Syzygium cumini) against fruit borers, Meridarchis scyrodes Meyrick and Dudua aprobola (Meyrick) in semi- arid region. International Conference on Entomology organized by Punjabi University, Patiala during 03 to 05, December 2016.
Haldhar SM, Sinha B Choudhary BR, Singh D, Konsam J and Thaochan, N. 2023b. Plant-insect interaction in underutilized horticultural crops for sustainable production. Journal of Agriculture and Ecology, 17: 1-13; https: // doi.org/10.58628/JAE-2317-301.
Halubanza B. 2024. A framework for an early warning system for the management of the spread of locust invasion based on artificial intelligence technologies (Doctoral dissertation: The University of Zambia.
Hameed A, Qazi M, Rafiq MU, Akhtar H 2025 Fungal endophytes and soilborne fungi. Fungal endophytes volume II: applications in agroecosystems and plant protection. Springer Nature Singapore, pp 485–508.
Hayden KJ, Garbelotto M, Knaus BJ, Cronn RC, Rai H, Wright JW. 2014. Dual RNA-seq of the plant pathogen Phytophthora ramo¬rum and its tanoak host. Tree Genet Genom.10: 489–502.
He W, Xu W, Xu L, Fu K, Guo W, Bock R, Zhang J.(2020). Length-dependent accumulation of double-stranded RNAs in plastids affects RNA interference efficiency in the Colorado Potato Beetle. J. Exp. Bot. 71, 2670–2677.
Heeb L, Jenner E & Cock MJW. 2019. Climate-smart pest management: building resilience of farms and landscapes to changing pest threats. J Pest Sci, 92: 951–969. https://doi.org/10.1007/s10340-019-01083-y.
Herrera-Estrella A. 2014. Genome-wide approaches toward understanding mycotrophic Trichoderma species. In: Gupta V, Schmoll M, Herrera-Estrella A, Upadhyay RS, Tuohy MG, editors. Biotechnology and biology of Trichoderma. Oxford: Else¬vier; p. 455–64.
Hickey L T, Hafeez N, Robinson H, Jackson S A, Leal-Bertioli S, Tester M, et al. 2019. Breeding crops to feed 10 billion. Nat. Biotechnol. 37, 744–754. doi: 10.1038/s41587-019-0152-9.
Hillnhütter C, Mahlein A K, Sikora R A, and Oerke E C. 2011. Remote sensing to detect plant stress induced by Heterodera schachtii and Rhizoctonia solani in sugar beet fields. Field Crop Res. 122, 70–77. doi: 10.1016/j.fcr.2011.02.007.
Holzinger A, Keiblinger K, Holub P, Zatloukal K, and Müller H. 2023. AI for life: trends in artificial intelligence for biotechnology. New Biotechnol. 74, 16–24. doi: 10.1016/j.nbt.2023.02.001.
Huss CP, Holmes KD & Blubaugh CK. 2022. Benefits and risks of intercropping for crop resilience and pest management. Journal of Economic Entomology, 115 (5): 1350-1362.
Ilieva T, Karova A and Ivanova M. 2025. Sustainable agriculture through integrated pest management: strategies for effective implementation. In: Nathanail, E.G., Gavanas, N., Adamos, E. (eds) Climate Crisis and Resilient Transportation Systems. CSUM 2024. Lecture Notes in Intelligent Transportation and Infrastructure. Springer, Cham. https: //doi.org/10.1007/978-3-031- 82818-8_38.
Jain A, Sarsaiya S, Singh R, Gong Q, Wu Q, & Shi J. 2024. Omics approaches in understanding the benefits of plant-microbe interactions. Frontiers in Microbiology, 15, 1391059. https://doi.org/10.3389/fmicb.2024.1391059.
Jain A, Singh HB and Das S. 2021. Deciphering plant-microbe crosstalk through proteomics studies. Microbiological Research, 242: 126590, https://doi.org/10.1016/j.micres.2020.126590.
Jiang CH, Yao XF, Mi DD, Li ZJ, Yang BY, Zheng Y, Ql YJ, Guo JH. 2019. Comparative transcriptome analysis reveals the biocontrol mechanism of Bacillus velezensis F21 against Fusarium wilt on watermelon. Front Microbiol. https://doi.org/10.3389/fmicb.2019.00652.
Kage U, Karre S, Kushalappa AC, McCartney C. 2017. Identification and characterization of a fusarium head blight resistance gene TaACT in wheat QTL-2DL. Plant Biotechnol J. 15(4): 447–57. https://doi.org/10.1111/pbi.12641.
Kashyap N, Singh SK, Yadav N, Singh VK, Kumari M, Kumar D, Kumar A 2023 Biocontrol screening of endophytes: applications and limitations. Plants. 12(13):2480.
Kaur J, Sahu K P, and Singh S. 2022. Optimization of pest management using artificial intelligence: fundamentals and applications, vol. 11: Souvenir & Abstracts.
Keppanan R, Karuppannasamy A, Nagaraja B, Thiruvengadam V, Kesavan S, Dhawane Y, Ramasamy A.(2024). Effectiveness of chitosan nano hydrogel mediated pickering encapsulation of EcR dsRNA against the Whitefly, Bemisia Tabaci Asia-I (Gennedius)(Hemiptera: Aleyordidae). Pestic. Biochem. Physiol. 198, 105712.
Khan MA, Gupta D, Siddiqui ZH, Alam P & Panda SK. 2025. Advancing crop resilience: integrating multi-omics approaches for abiotic stress tolerance. In: Panda, S.K., Khan, M.A. (eds) Plant Functional Genomics for Abiotic Stress Resilience. Plant in Challenging Environments, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-032-01704-8_7.
Kim ST, Kim SG, Kang YH, Wang Y, Kim JY, Yi N, Kim JK, Rakwal R, Koh HJ, Ky K. 2008. Proteomics analysis of rice lesion mimic mutant (spl1) reveals tightly localized probenazole-induced protein (PBZ1) in cells undergoing programmed cell death. J Proteome Res. 7: 1750–60.
Kimotho RN & Maina S. 2024. Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers?. Journal of Experimental Botany, 75 (5): 1289-1313.
Kumar R, Kumar M, Chaudhary V. et al. 2025. Exploring recent advances, limitations, and future prospects of OMICS-based technologies in plant-pathogen interaction studies: a systematic review. Discovery Plants, 2: 284. https://doi.org/10.1007/s44372-025-00337-7.
Kumar R, Yadav MK, Yadav SL, Kumar M, Sharma AK, Tripathi MK. 2023. Bioinformatics and omics for crop improvement. Octa J Biosci. 11(1): 24–39.
Kumari P, Bhatt A, Meena VK, Adhikari S, Dhar N, Chawda H, Chand S, Joshi P, Mangal V, Sood S. 2024. Plant phenomics: the force behind tomorrow’s crop phenotyping tools. J Plant Growth Regul. https://doi.org/10.1007/s00344-024-11450-4.
Kusari S, Kosuth J, Cellarova E, and Spiteller M. 2011. Survival strategies of endophytic Fusarium solani against indigenous camptothecin biosynthesis. Fungal Ecology. 4(3): 219–223.
Lashin I, Fouda A, Gobouri AA, Azab E, Mohammedsaleh ZM, Makharita RR 2021 Antimicrobial and in vitro cytotoxic efficacy of biogenic silver nanoparticles (Ag-NPs) fabricated by callus extract of Solanum incanum L. Biomolecules. 11(3):341.
Lee B-M, Park Y-J, Park D-S, Kang H-W, Kim J-G, Song E-S, Park I-C, Yoon U-H, Hahn J-H, Koo B-S, Lee G-B, Kim H, Park H-S, Yoon K-O, Kim J-H, Jung C-H, Koh N-H, Seo J-S, Go S-J. 2005. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res. 33: 577–86. https://doi.org/10.1093/nar/gki206.
Leonard SP, Powell JE, Perutka J, Geng P, Heckmann LC, Horak RD, Davies BW, Ellington AD, Barrick JE, Moran NA. (2020). Engineered symbionts activate honey bee immunity and limit pathogens. Science 367, 573–576.
Li J, Shi Y, Xue Q, Smagghe G, De Schutter K, Taning CNT.(2024). Identification and functional analysis of gut dsRNases in the beet armyworm Spodoptera exigua. Insect Biochem. Mol. Biol. 175, 104206.
Li Y H, Zhou G, Ma J, Jiang W, Jin, L G, Zhang Z, et al. 2014. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32, 1045–1052. doi: 10.1038/nbt.2979.
Li Z, Sun J, Shen Y, Yang Y, Wang X, Wang X, Tian P, Qian Y.2024. Deep migration learning-based recognition of diseases and insect pests in Yunnan tea under complex environments. Plant Methods 20:101. doi: 10.1186/s13007-024-01219-x.
Lins E C, Belasque J and Marcassa L G. 2009. Detection of citrus canker in citrus plants using laser induced fluorescence spectroscopy. Precis. Agric. 10, 319–330. doi: 10.1007/s11119-009-9124-2.
Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shafer BT, Elbourne LD, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, vandeMortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. 2012. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multi-trophic interactions. PLoS Genet.; 8: e1002784.
Lopes T, Hatt S, Xu Q, Chen J, Liu Y & Francis F. 2016. Wheat (Triticum aestivum L.)-based intercropping systems for biological pest control. Pest Manage. Sci., 72: 2193-2202
Loraine AE, McCormick S, Estrada A, Patel K, Qin P. 2013. RNA-seq of Arabidopsis pollen uncovers novel transcription and alterna¬tive splicing. Plant Physiol.; 162: 1092–109.
Lu Y, Yi S, Zeng N, Liu Y, Zhang Y.. 2017. Identification of rice diseases using deep convolutional neural networks. Neurocomputing 267, 378 384. doi: 10.1016/j.neucom.2017.06.023.
Mahanta DK, Komal J, Bhoi TK et al.(2025). RNA interference (RNAi) for insect pest management: understanding mechanisms, strategies, challenges and future prospects. BIOLOGIA FUTURA 76, 465–477 https://doi.org/10.1007/s42977-025-00281-3.
Marra R, Ambrosino P, Carbone V, Vinale F, Woo SL, Ruocco M, Ciliento R, Lanzuise S, Ferraioli S, Soriente I, Gigante S, Turra D, Fogliano V, Scala F, Lorito M. 2006. Study of the three-way interaction between Trichoderma atroviride, plant and fungal patho¬gens by using a proteomic approach. Curr Genet.; 50: 307–21.
Marrone P G. 2025. Increasing the use of biological pesticides in integrated pest management programs. Frontiers in Insect Science, 5, 1552361. https://doi.org/10.3389/finsc.2025.1552361
Marrone PG. 2019. Pesticidal natural products – status and future potential. Pest Manag Sci., 75: 2325–40. doi: 10.1002/ps.5433
Maurice S, Montes MS, Nielsen BJ, Bødker L, Martin MD, Jønck CG, Kjøller R, Rosendahl S. 2019. Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity. Mol Plant Pathol.; 20(8): 1134–46. https://doi.org/10.1111/mpp.12819.
Mawcha KT, Kinyanjui G, Simiyu SW, Babalola OO and Ndolo DO. 2024. Biopesticides for Sustainable Agriculture: A Review of Their Role in Integrated Pest Management. Agricultural Sciences. IntechOpen. doi:10.5772/intechopen.1006277.
Mena E, Garaycochea S, Stewart S, Montesano M, Ponce De León I. 2022. Comparative genomics of plant pathogenic Diaporthe species and transcriptomics of Diaporthe caulivora during host infection reveal insights into pathogenic strategies of the genus. BMC Genomics.; 23(1): 175.
Mendoza-Alatorre M, Julian-Chávez B., Solano-Ornelas S, Siqueiros-Cendón TS, Torres-Castillo JA, et al. 2025. RNAi in pest control: critical factors affecting dsRNA efficacy. Insects, 16(7), 737; https://doi.org/10.3390/insects16070737.
Mihrete TB & Mihretu FB. 2025. Crop diversification for ensuring sustainable agriculture, risk management and food security. Global Challenges, 9 (2), 2400267.
Mishra B, Kumar N & Mukhtar MS. 2019. Systems biology and machine learning in plant–pathogen interactions. Molecular Plant-Microbe Interactions, 32: 4555.
Mitrofanova O, and Khakimova A. 2017. New genetic resources in wheat breeding for increased grain protein content. Russ. J. Genet. 7, 477–487. doi: 10.1134/S2079059717040062.
Murmu S, Pradhan A K, Chaurasia H, Kumar D and Samal I. 2022. Impact of bioinformatics advances in agricultural sciences. AgroSci. Today 3, 480–485.
Murovec J, Pirc Z and Yang B. 2017. New variants of CRISPR RNA-guided genome editing enzymes. Plant Biotechnol. J. 15, 917–926. doi: 10.1111/pbi.12736.
Nansen C, Ribeiro L P, Dadour I and Roberts J D. 2015. Detection of temporal changes in insect body reflectance in response to killing agents. PLoS One 10:e0124866. doi: 10.1371/journal.pone.0124866.
Nazir A, Puthuveettil AR, Hussain FHN, Hamed KE, Munawar N 2024 Endophytic fungi: nature’s solution for antimicrobial resistance and sustainable agriculture. Front Microbiol 15:1461504.
Niazi P, Monib AW, Ozturk H, Mansoor M, Azizi A, Hassand MH et al. 2023. Review on surface elements and bacterial biofilms in plant-bacterial associations. J. Res. Appl. Sci. Biotechnol. 2, 204–214. 10.55544/jrasb.2.1.30.
Niu J, Chen R, Wang JJ.(2024). RNA interference in insects: The link between antiviral defense and pest control. Insect Sci. 31, 2–12.
Ownley BH, Gwinn KD and Vega FE. 2010. Endophytic fungal entomopathogens with activity against plant pathogens: ecology and evolution. BioControl. 55 (1): 113-128.
Pandey K, Saharan B.S.2025. Soil microbiomes: a promising strategy for boosting crop yield and advancing sustainable agriculture. Discover Agriculture, 3: 54 . https://doi.org/10.1007/s44279-025-00208-5.
Pandey PK, Samanta R, Yadav RNS 2019 Inside the plant: addressing bacterial endophytes in biotic stress alleviation. Arch Microbiol 201:415–429.
Park Y H, Choi S H, Kwon Y J, Kwon S W, Kang Y J, and Jun T H. 2023. Detection of soybean insect pest and a forecasting platform using deep learning with unmanned ground vehicles. Agronomy 13:477. doi: 10.3390/agronomy13020477.
Parveen SS and Rashtrapal PS. 2024. Integrated Pest management strategies using endophytic entomopathogenic fungi. Plant Science Today, 568-574. DOI: 10.14719/pst.2740
Pinter P J Jr, Hatfield J L, Schepers J S, Barnes E M, Moran M S, Daughtry C S et al. 2003. Remote sensing for crop management. Photogramm. Eng. Remote. Sens. 69, 647–664. doi: 10.14358/PERS.69.6.647.
Polder G, Blok P M, De Villiers H A, Van Der Wolf J M and Kamp J. 2019. Potato virus Y detection in seed potatoes using deep learning on hyperspectral images. Front. Plant Sci. 10:209. doi: 10.3389/fpls.2019.00209.
Prabhakar M, Prasad Y G and Rao M N. 2012. “Remote sensing of biotic stress in crop plants and its applications for pest management” in Crop stress and its management: Perspectives and strategies (New York: Springer), 517–549.
Rai K, Hash C, Singh A K and Velu G. 2008. Adaptation and quality traits of a germplasm-derived commercial seed parent of pearl millet. Plant Genetic Resour. Newslett. 154, 20–24.
Rathnasamy SA, Gothandapani S, Chellamuthu S, Chakraborty A, Gurusamy D, Roy A, et al. 2023. Omics technologies unravelling the plant-pathogen interaction and stress response. In: Mani A, Kushwaha S, editors, et al., Genomics of plant-pathogen interaction and the stress response. CRC Press; p. 74–110. https://doi.org/10.1201/9781003153481.
Sahoo A, Yadav G, Mehta T et al. 2025. Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture. Discov Sustain, 6: 659 https://doi.org/10.1007/s43621-025-01582-2
Samadia D & Haldhar S. 2017. Breeding strategies and scope of improvement in arid zone fruit crop-plants under abiotic stressed agro-climate: an analysis. Journal of Agriculture and Ecology, 4: 1–13.
Sana TR, Fischer S, Wohlgemuth G, Katrekar A, Jung KH, Ronald PC, Fiehn O. 2010. Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv Oryzae. Metabolomics.; 6: 451–65.
San-Miguel K, Scott J G. 2016. The next generation of insecticides: dsRNA is stable as a foliar-applied insecticide. Pest Manag. Sci. 72, 801–809. doi: 10.1002/ps.4056.
Serumaga J P, Beyene Y, Pillay K, Kullaya A, Oikeh S O, Mugo S et al. 2018. Grain-yield stability among tropical maize hybrids derived from doubled-haploid inbred lines under random drought stress and optimum moisture conditions. Crop Past. Sci. 69, 691–702. doi: 10.1071/CP17348.
Sharma R, Arya S, & Singh R. 2025. Pesticides and their effects on pollinators. IJES, 16(2): 110–119.
Shen FT, Yen JH, Liao CS, Chen WC, and Chao YT. 2019. Screening of rice endophytic biofertilizers with fungicide tolerance and plant growth-promoting characteristics. Sustainability. 11(4): 1133. https://doi.org/10.3390/su11041133.
Shen Q & G Chu. 2004. Bi-directional nitrogen transfer in an intercropping system of peanut with rice cultivated in aerobic soil. Biol. Fertil. Soils, 40: 81-87.
Small I M, Joseph L and Fry W E. 2015) Development and implementation of the BlightPro decision support system for potato and tomato late blight management. Comput. Electron. Agric. 115, 57–65. doi: 10.1016/j.compag.2015.05.010.
Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G. 2006. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. ;78(3):779–87. https://doi.org/10.1021/ac05437y.
Sood M, Kapoor D, Kumar V, Kalia N, Bhardwaj R, Sidhu GP, Sharma A 2021. Mechanisms of plant defense under pathogen stress: a review. Curr Protein Pept Sci .22(5):376–395.
Spinelli F, Noferini M and Costa G. 2006. Near infrared spectroscopy (NIRs): perspective of fire blight detection in asymptomatic plant material. Proceeding of 10th international workshop on fire blight. Acta Hortic. 704, 87–90. doi: 10.17660/ActaHortic.2006.704.9.
Stetter M G, Zeitler L, Steinhaus A, Kroener K Biljecki M and Schmid K J. 2016. Crossing methods and cultivation conditions for rapid production of segregating populations in three grain amaranth species. Front. Plant Sci. 7:816. doi: 10.3389/fpls.2016.00816.
Stotz HU, Mitrousia GK, de Wit PJ, Fitt BD. 2014. Effector-triggered defence against apoplastic fungal pathogens. Trends Plant Sci. 19: 491–500.
Suciatmih and Rahmansyah M. 2013. Endophytic fungi isolated from mangrove plant and have antagonism role against Fusarium wilt. Journal of agricultural and Biological Science. 8 (3): 253-257.
Tahara ST, Mehta A, Rosato YB. 2003. Proteins induced by Xanthomonas axonopodispv. passiflorae with leaf extract of the host plant (Passiflorae edulis). Proteomics.; 3: 95–102.
Taracena ML, Oliveira PL, Almendares O, Umana C, Lowenberger C, Dotson EM, Paiva-Silva GO, Pennington PM.(2015). Genetically modifying the insect gut microbiota to control Chagas disease vectors through systemic RNAi. PLoS Negl. Trop. Dis. 9, e0003358.
Tiwari P, Bose SK, Park KI, Dufosse L & Fouillaud M. 2024. Plant-microbe interactions under the extreme habitats and their potential applications. Microorganisms,12: 448.
Trimmer M. 2024. Major forces driving biocontrol market expansion worldwide, in: Annual Biocontrol Industry Meeting (ABIM), Basel.
Van Emon JM. 2016. The omics revolution in agricultural research. J Agric Food Chem. 64(1): 36–44.
Varshney R K, Bohra A, Yu J, Graner A, Zhang Q and Sorrells M E. 2021. Designing future crops: genomics-assisted breeding comes of age. Trends Plant Sci. 26, 631–649. doi: 10.1016/j.tplants.2021.03.010.
Voss-Fels K P, Stahl A, and Hickey L T. 2019. Q&A:moderncropbreeding for future food security. BMC Biol. 17:18. doi: 10.1186/s12915-019-0638-4.
Waltz E. 2016. CRISPR-edited crops free to enter market, skip regulation. Nat. Biotechnol. 34:582. doi: 10.1038/nbt0616-582.
Watson A, Ghosh S, Williams M J, Cuddy W S, Simmonds J, Rey M D, et al. 2018. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat. Plants.4, 23–29. doi: 10.1038/s41477-017-0083-8.
Whitten M, Facey PD, Del Sol R, Fernández-Martínez LT, Evans MC, Mitchell JJ, Bodger OG, Dyson PJ.(2016). Symbiont-mediated RNA interference in insects. Proc. R. Soc. B Biol. Sci. 283, 20160042.
Wójcik-Jagła M, Rapacz M, Dubas E, Krzewska M, Kope´c P, Nowicka A, et al. 2020. Candidate genes for freezing and drought tolerance selected on the basis of proteome analysis in doubled haploid lines of barley. Int. J. Mol. Sci. 21:2062. doi: 10.3390/ijms21062062.
Xiao Q, Bai X, Zhang C, He Y. 2022. Advanced high-throughput plant phenotyping techniques for genome-wide association studies: a review. J Adv Res.; 35: 215–30.
Xiao Q, Li W, Kai Y, Chen P, Zhang J and Wang B. 2019. Occurrence prediction of pests and diseases in cotton on the basis of weather factors by long short term memory network. BMC Bioinform. 20, 1–15. doi: 10.1186/s12859-019-3262-y.
Xu H R, Ying Y B, Fu X P and Zhu S P. 2007. Near-infrared spectroscopy in detecting leaf miner damage on tomato leaf. Biosyst. Eng. 96, 447–454. doi: 10.1016/j.biosystemseng.2007.01.008.
Xu X, et al. 2022. The role of metabolomics in understanding plant defense mechanisms against pathogens. Metabolites.; 12(7): 633. https://doi.org/10.3390/metabo12070633.
Xu Z, Li C, Zhang C, Yu Y, van der Werf W & Zhang F. 2020. Intercropping maize and soybean increases efficiency of land and fertilizer nitrogen use; a meta-analysis. Field Crops Res., 246: 107661.
Yang W, Wang B, Lei G, Chen G, Liu D..2022. Advances in nanocarriers to improve the stability of dsRNA in the environment. Front. Bioeng. Biotechnol. 10, 974646.
Yin R, Xia K, Xu X. 2023. Spatial transcriptomics drives a new era in plant research. Plant J.; 116(6): 1571–81.
Yones M S, Arafat S, Abou Hadid A F, Abd Elrahman H A and Dahi H F. 2012. Determination of the best timing for control application against cotton leaf worm using remote sensing and geographical information techniques. Egypt. J. Remote Sens. Space Sci. 15, 151–160. doi: 10.1016/j.ejrs.2012.05.004.
Zaman NR, Chowdhury UF, Reza RN, Chowdhury FT, Sarker M, Hossain MM, Akbor MA, Amin A, Islam MR and Khan H. 2021. Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition. Public library of science one. 16 (9): 0257863.
Zhang F, Chen H, Zhang X, Gao C, Huang J, Lü L, Shen D, Wang L, Huang C, Ye W, Zheng X, Wang Y, Vossen JH, Dong S. 2021. Genome analysis of two newly emerged potato late blight isolates sheds light on pathogen adaptation and provides tools for disease management. Phytopathology. ;111(1):96–107. https://doi.org/10.1094/PHYTO-05-20-0208-FI.
Zhang X, Han L, Dong Y, Shi Y, Huang W, Han L et al. 2019. A deep learning-based approach for automated yellow rust disease detection from high-resolution hyperspectral UAV images. Remote Sensing 11:1554. doi: 10.3390/ rs11131554.
Zhao H, Zhou T, Xie J, Cheng J, Chen T, Jiang D, Fu Y. 2020. Mycoparasitism illuminated by genome and transcriptome sequenc¬ing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum. Microb Genom.; 6(3): 6.
Zotti M J, Smagghe G. 2015. RNAi technology for insect management and protection of beneficial insects from diseases: lessons, challenges and risk assessments. Neotrop. Entomol. 44, 197–213. doi: 10.1007/s13744-015-0291-8.
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