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Multi-omics approaches for plant disease diagnosis and resilience

Guest Editors:
Sunil S. Gangurde, PhD: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Manish Pandey, PhD: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Youxiong Que, PhD: Fujian Agriculture and Forestry University, China



In nature, plants are constantly exposed to microorganisms and pests, some of which can be pathogenic. Plant diseases can have a strong environmental and economic impact, and represent a major threat to food security due to crop yield losses. This is especially true under the extreme weather conditions associated with climate change, which affect the response of plants to abiotic and biotic stress, including infectious diseases. The occurrence and spreading of plant diseases demand major efforts to understand how and why the pathogenesis occurs, and improve the available strategies for plant disease diagnosis, management and resistance. BMC Plant Biology launched the collection Multi-omics approaches for plant disease diagnosis and resilience. We present manuscripts on novel research and applications where multi-omics methods are applied to improve disease diagnosis and resilience in plants. This collection highlights the importance and potential challenges of developing and integrating multi-omics technologies to take a holistic approach on plant pathogenesis, plant disease diagnosis and control, and ultimately plant disease resistance.

Meet the Guest Editors

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Sunil S. Gangurde: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India

Dr Gangurde completed his PhD at the International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India. During the PhD he worked in the area of peanut genomics and established genomic tools useful for developing disease resistance in peanuts. Currently, he is working as Post-Doctoral Research Associate at the University of Georgia, Tifton, USA. During the postdoc he is leading the pangenome initiative of Aspergillus flavus, a fungus that produces aflatoxins especially in peanut and corn. Dr Gangurde has published close to 50 research articles in various international peer-review journals, and he is serving as an editorial board member of several international journals including BMC Plant Biology.

Manish Pandey: International Crops Research Institute for the Semi-Arid Tropics, India

Dr Pandey is currently leading the Groundnut and Pigeon pea Genomics, Prebreeding & Bioinformatics group at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. His key contributions include developing and deploying genomic resources for breeding climate-resilient and  high-nutritional-value crop varieties. He has published more than 170 scientific articles (>8000 citations) in various international journals, including Nature Genetics, PNAS and Molecular Plant. Recognizing his contribution, he has now been inducted in many scientific academies of India, as Fellow of The National Academy of Agricultural Sciences (New Delhi) and Telangana Academy of Agricultural Sciences (Telangana).

Youxiong Que: College of Agriculture, Fujian Agriculture and Forestry University, China

Dr Que is a full Professor in the College of Agriculture at the Fujian Agriculture and Forestry University (FAFU). He was employed as an assistant professor in 2008, promoted to be an associate professor in 2010 and a professor in 2015. He has been a visiting scientist at USDA-ARS during 2010-2011. He is now the director of Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs / FAFU, China. His research interests are in the fields of crop genetics and biotechnology, especially sugarcane biotechnology, including but not limited to the following three aspects: molecular interactions between crops and pathogens, gene mining and function identification, and molecular breeding. Dr Que serves as an editorial board member for several eminent journals including BMC Plant Biology.

About the collection

In nature, plants are constantly exposed to microorganisms and pests, some of which can be pathogenic. Plant diseases can have a strong environmental and economic impact, and represent a major threat to food security due to crop yield losses. This is especially true under the extreme weather conditions associated with climate change, which affect the response of plants to abiotic and biotic stress, including infectious diseases. The occurrence and spreading of plant diseases demand major efforts to understand how and why the pathogenesis occurs, and improve the available strategies for plant disease diagnosis, management and resistance.

Advances in next-generation sequencing technologies enabled the emergence of different omics technologies, such as genomics, transcriptomics, metabolomics, proteomics, phenomics and ionomics. Multiple-omics approaches have been applied to plant systems for developing effective diagnostic tools for plant diseases and better understanding plants' response to disease. When implemented and integrated, multiple-omics methods can provide a ‘holistic picture’ that can reveal how plants sense, respond to and eliminate disease-causing (micro) organisms. They can therefore be essential in revealing the mechanisms underlying plant-microbial interactions, developing effective diagnostic tools for plant diseases, and bioengineering genetic control strategies for disease resilience in plants.

To acknowledge the relevance of this research field in the context of achieving sustainable food security for the future (The United Nation’s Sustainable Development Goals 2 (SDG2), ‘Zero hunger’), BMC Plant Biology launched the collection Multi-omics approaches for plant disease diagnosis and resilience. We present manuscripts on novel research and applications where multi-omics methods are applied to improve disease diagnosis and resilience in plants. This collection highlights the importance and potential challenges of developing and integrating multi-omics technologies to take a holistic approach on plant pathogenesis, plant disease diagnosis and control, and ultimately plant disease resistance.

Our collection showcases research articles and methods exploring a broad range of research areas, including the following topics:

  • Application and integration of omics technologies (e.g. genomics, meta-genomics, transcriptomics, metabolomics, proteomics) for plant disease diagnosis and resilience
  • Genomes and pangenomes of disease-causing pathogens, and pan-genome-wide association (pan-GWAS) studies to uncover unknown virulence genes
  •  Pathogenicity-associated genes in bacterial and fungal pathogens
  • Host-induced gene silencing (HIGS) and spray induced gene silencing (SIGS) using RNA silencing mechanisms to manage pathogens in the field
  • Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) to identify plant disease resistance loci or genes
  • Population genomics of plant pathogens
  •  Genomics-assisted breeding of crop varieties for disease resistance
  •  Multi-omics approaches applied to plant-pathogen interactions
  • Molecular crosstalk between host and pathogen during infection
  •  Plant-microbiome crosstalk to improve disease resilience in plants
  • Development of diagnostic markers for pathogen identification and rapid disease diagnosis
  • Plant phenomics and ionomics applied to plant disease diagnosis and resilience


Image credit: Production Perig / stock.adobe.com

  1. The quality of groundnut produce is adversely impacted due to aflatoxin contamination by the fungus Aspergillus flavus. Although the transcriptomic control is not fully understood, the interaction between long no...

    Authors: Pushpesh Joshi, Vinay Sharma, Arun K. Pandey, Spurthi N. Nayak, Prasad Bajaj, Hari K. Sudini, Shailendra Sharma, Rajeev K. Varshney and Manish K. Pandey
    Citation: BMC Plant Biology 2025 25:345
    Content type: Research Published on:

  2. The Oleaceae family, encompassing key genera such as Fraxinus (ash trees), Olea (olives), Jasminum (jasmine), Syringa (lilac), and Forsythia, plays a crucial ecological and economic role. Despite their importance...

    Authors: Saba Parvez, Maryam Asif, Alizay Ahmad, Iqra Javaid, Muhammad Zaman Rasheed, Romana Iftikhar, Nada H. Aljarba, Rabia Zafar, Aqsa sarwar, Rao Sohail Ahmed Khan and Saad Serfraz
    Citation: BMC Plant Biology 2025 25:259
    Content type: Research Published on:

  3. Globally, rice bacterial blight disease causes significant yield losses. Metabolomics is a vital tool for understanding this disease by analyzing metabolite levels and pathways involved in resistance and susce...

    Authors: Prajna Priyadarshini Das, Aman Kumar, Mujahid Mohammed, Komal Bhati, Komaragiri Rajesh Babu, Kailash Pati Bhandari, R. M. Sundaram and Irfan Ahmad Ghazi
    Citation: BMC Plant Biology 2025 25:178
    Content type: Research Published on:

  4. m6A RNA modifications are the most prevalent internal modifications in eukaryotic mRNAs and are crucial for plant growth and development, as well as for responses to biotic or abiotic stresses. The modificatio...

    Authors: Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui and Jun Cao
    Citation: BMC Plant Biology 2025 25:147
    Content type: Research Published on:

  5. Thaumatin-like proteins (TLPs) are crucial pathogenesis-related proteins that significantly contribute to plant defense rection. Fusarium oxysporum f. sp. cubense (Foc) causes Fusarium wilt of bananas, a serious ...

    Authors: Yi-le Huo, Si-wen Liu, Huo-qing Huang, Zai-yuan Li, Mudassar Ahmad, Meng-xia Zhuo, Wen-juan Chen, Chun-yu Li, Bo Liu and Ya-dong Li
    Citation: BMC Plant Biology 2025 25:90
    Content type: Research Published on:

  6. Poa pratensis is a predominant cool-season turfgrass utilized in urban landscaping and ecological management. It is extensively employed in turf construction and in the regulation of ecological environments. Howe...

    Authors: Wenke Dong, Yujuan Zhang, Yan Wang and Chunxu Zhao
    Citation: BMC Plant Biology 2024 24:1195
    Content type: Research Published on:

  7. Sooty mold (SM), caused by Cladosporium species, is a pervasive threat to tea plant health, affecting both canopy structure and crop yield. Despite its significance, understanding the complex interplay between de...

    Authors: Shuangshuang Wang, Yang Xu, Jiazhi Shen, Hao Chen, Yu Wang and Zhaotang Ding
    Citation: BMC Plant Biology 2024 24:1079
    Content type: Research Published on:

  8. Bacterial wilt (BW), caused by Ralstonia solanacearum (Ral), results in substantial yield losses in pepper crops. Developing resistant pepper varieties through breeding is the most effective strategy for managing...

    Authors: Ji-Su Kwon, Junesung Lee, Jayabalan Shilpha, Hakgi Jang and Won-Hee Kang
    Citation: BMC Plant Biology 2024 24:1036
    Content type: Research Published on:

  9. Rapeseed (Brassica napus L.) is an important oil and industrial crop worldwide. Black rot caused by the bacterial pathogen Xanthomonas campestris pv. campestris (Xcc) is an infectious vascular disease that leads ...

    Authors: Li Yang, Lingli Yang, Chuanji Zhao, Zetao Bai, Meili Xie, Jie Liu, Xiaobo Cui, Klaas Bouwmeester and Shengyi Liu
    Citation: BMC Plant Biology 2024 24:1027
    Content type: Research Published on:

  10. Septoria tritici blotch (STB) disease causes yield losses of up to 50 per cent in susceptible wheat cultivars and can reduce wheat production. In this study, genomic architecture for adult-plant STB resistance...

    Authors: Madhu Patial, Sudhir Navathe, Xinyao He, Umesh Kamble, Manjeet Kumar, Arun Kumar Joshi and Pawan Kumar Singh
    Citation: BMC Plant Biology 2024 24:846
    Content type: Research Published on:

  11. ‘Hongyang’ kiwifruit (Actinidia chinensis cv ‘Hongyang’) is a high-quality variety of A. chinensis with the advantages of high yield, early ripening, and high stress tolerance. Studies have confirmed that the Sha...

    Authors: Yinqiang Zi, Zhiming Zhang, Ke Zhao, Xiuyao Yang, Ling Zhu, Tuo Yin, Chaoying Chen, Ke Wen, Xulin Li, Hanyao Zhang and Xiaozhen Liu
    Citation: BMC Plant Biology 2024 24:833
    Content type: Research Published on:

  12. Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-...

    Authors: Kalpana Singh, Pradeep Sharma, Sarika Jaiswal, Pallavi Mishra, Ranjeet Maurya, Senthilkumar K Muthusamy, MS Saharan, Rahul Singh Jasrotia, Jitender Kumar, Shefali Mishra, Sonia Sheoran, GP Singh, UB Angadi, Anil Rai, Ratan Tiwari, Mir Asif Iquebal…
    Citation: BMC Plant Biology 2024 24:676
    Content type: Research Published on:

  13. The sorghum aphid Melanaphis sacchari (Zehntner) (Homoptera: Aphididae) is an important insect in the late growth phase of sorghum (Sorghum bicolor L.). However, the mechanisms of sorghum response to aphid infest...

    Authors: Xin-Rui Zhao, Dong-Ting Zhao, Ling-Yu Zhang, Jin-Hua Chang and Jiang-Hui Cui
    Citation: BMC Plant Biology 2024 24:529
    Content type: Research Published on:

  14. Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under dive...

    Authors: Hanif Khan, Gopalareddy Krishnappa, Sudheer Kumar, Narayana Bhat Devate, Nagenahalli Dharmegowda Rathan, Satish Kumar, Chandra Nath Mishra, Sewa Ram, Ratan Tiwari, Om Parkash, Om Parkash Ahlawat, Harohalli Masthigowda Mamrutha, Gyanendra Pratap Singh and Gyanendra Singh
    Citation: BMC Plant Biology 2024 24:411
    Content type: Research Published on:

  15. Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, w...

    Authors: Sunil S. Gangurde, Walid Korani, Prasad Bajaj, Hui Wang, Jake C. Fountain, Gaurav Agarwal, Manish K. Pandey, Hamed K. Abbas, Perng-Kuang Chang, C. Corley Holbrook, Robert C. Kemerait, Rajeev K. Varshney, Bhabesh Dutta, Josh P. Clevenger and Baozhu Guo
    Citation: BMC Plant Biology 2024 24:354
    Content type: Research Published on:

  16. Two-tiered plant immune responses involve cross-talk among defense-responsive (DR) genes involved in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), effector-triggered immunity (ETI) and ef...

    Authors: Yunya Bi, Yue Yu, Shuaige Mao, Tao Wu, Tao Wang, Ying Zhou, Kabin Xie, Hua Zhang, Li Liu and Zhaohui Chu
    Citation: BMC Plant Biology 2024 24:347
    Content type: Research Published on:

  17. Aconitum carmichaelii Debx. has been widely used as a traditional medicinal herb for a long history in China. It is highly susceptible to various dangerous diseases during the cultivation process. Downy mildew is...

    Authors: Lijuan Chen, Yiwen Hu, Li Huang, Long Chen, Xianglei Duan, Guangzhi Wang and Hong Ou
    Citation: BMC Plant Biology 2024 24:332
    Content type: Research Published on:

  18. Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for ind...

    Authors: Manish K. Pandey, Sunil S. Gangurde, Yaduru Shasidhar, Vinay Sharma, Sandip M. Kale, Aamir W. Khan, Priya Shah, Pushpesh Joshi, Ramesh S. Bhat, Pasupuleti Janila, Sandip K. Bera and Rajeev K. Varshney
    Citation: BMC Plant Biology 2024 24:262
    Content type: Research Published on:

    The Correction to this article has been published in BMC Plant Biology 2024 24:336

  19. Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA i...

    Authors: Yaqian Chen, Jinfeng Wu, Changrui Ma, Dawei Zhang, Dinggang Zhou, Jihong Zhang and Mingli Yan
    Citation: BMC Plant Biology 2024 24:245
    Content type: Research Published on:

  20. Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacill...

    Authors: Mushineni Ashajyothi, Shivannegowda Mahadevakumar, Y. N. Venkatesh, Pullabhotla V. S. R. N. Sarma, Chalasani Danteswari, Alexander Balamurugan, Ganesan Prakash, Vikas Khandelwal, C. Tarasatyavathi, Appa Rao Podile, Kirankumar S. Mysore and Siddaiah Chandranayaka
    Citation: BMC Plant Biology 2024 24:197
    Content type: Research Published on:

    The Correction to this article has been published in BMC Plant Biology 2024 24:264

  21. Grafting is widely used as an important agronomic approach to deal with environmental stresses. However, the molecular mechanism of grafted tomato scions in response to biotic stress and growth regulation has ...

    Authors: Ce Liu, Yanhong Jia, Lixia He, Hui Li, Jian Song, Lizhu Ji and Chunguo Wang
    Citation: BMC Plant Biology 2024 24:130
    Content type: Research Published on:

  22. The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in se...

    Authors: Alexander Balamurugan, Mallana Gowdra Mallikarjuna, Shilpi Bansal, S. Chandra Nayaka, Hosahatti Rajashekara, Tara Satyavathi Chellapilla and Ganesan Prakash
    Citation: BMC Plant Biology 2024 24:75
    Content type: Research Published on: