Enhancing genomic diversity for climate-resilient crops and their phytoecosystems, by engaging AI and genome editing

  • 79

    Total views and downloads

Participate in this topic

Submit your idea

You will be redirected to our submission process.

Submit your manuscript summarySubmit your manuscript

About this Research Topic

Submission deadlines

  1. Manuscript Summary Submission Deadline 1 March 2026 | Manuscript Submission Deadline 1 July 2026

  2. This Research Topic is currently accepting articles.

    1. Check author guidelines

Background

Advances in plant genomics are rapidly transforming the landscape of crop improvement. The emergence of pangenomics and progress in genotyping for genetic diversity analysis have revealed the full spectrum of variation within and across crop species, providing unprecedented insight into allelic and regulatory diversity. At the same time, artificial intelligence (AI) and machine learning (ML) tools enable data-driven prediction of complex genotype × environment interactions. Precision genome editing technologies, such as CRISPR-based methods, are redefining how breeders can manipulate key loci and regulatory networks. The convergence of these approaches presents a unique opportunity to design crops with enhanced resilience, productivity, and sustainability under changing climate conditions. We particularly encourage studies integrating plant genomic variation with symbiont and metagenomic data (e.g., rhizosphere/phyllosphere microbiomes, mycorrhizae, endophytes) to elucidate plant–microbe–environment interactions underpinning resilience and ecosystem services.

This Research Topic aims to explore pangenomic diversity to accelerate the development of climate-resilient crops by engaging AI-driven analytics, and genome editing approaches. Despite major genomic advances, translating genetic variation into usable breeding outcomes remains a significant challenge. By exploiting the comprehensive allelic variation revealed by pangenomes and the genetic diversity captured through high-throughput genotyping, combined with predictive AI models, breeders might more effectively identify and prioritize genes and alleles associated with tolerance to heat, drought, and salinity, as well as improved yield stability and nutrient-use efficiency. In parallel, genome editing technologies such as CRISPR-based methods offer precise and efficient tools to fine-tune adaptive traits associated with environmental resilience. The overarching goal is to establish an integrated, breeding-by-design framework capable of predicting, selecting, and engineering crop genotypes with enhanced stability and adaptability to future climate scenarios, while accounting for phytoecosystem dynamics and plant–symbiont interactions where relevant.

This Research Topic welcomes original research articles, reviews, and perspectives focusing on pangenomics, AI/machine learning, and genome editing for crop improvement. Areas of interest include (but are not limited to): pangenome construction and analysis; identification of adaptive alleles from wild relatives; AI-based genomic prediction and explainable models for genotype × environment interactions; CRISPR-based precision breeding; and multi-omics integration for trait dissection. We particularly welcome work that links genomic findings to mechanistic insights, including chromatin and epigenomic regulation of stress responses, structural variation and chromosome dynamics revealed by pangenomes, the roles of non-coding RNAs, and RNA processing in adaptation. Studies that integrate metagenomic or community-level data (e.g., plant-associated microbiomes and symbiont genomes) to analyze plant–microbe interactions within the phytoecosystem are encouraged.

Contributions addressing methodological innovations, computational pipelines, or comparative and evolutionary analyses (e.g., selection scans, domestication trajectories, structural variant evolution) across taxa are encouraged, provided they include comprehensive analysis beyond single-species gene-family catalogs. Organellar genome analyses should be integrated with nuclear genomic responses and phytoecologic context to be considered. Studies focused solely on quality traits, nutritional aspects, or soil quality must include a fundamental plant genomics basis and integration with broader phytoecosystem dynamics.

Rigor and reproducibility expectations:

o AI/ML: Clearly describe data partitioning (train/validation/test), prevent information leakage, report performance with appropriate metrics, include external or cross-environment validation where possible, and provide model interpretability/explainability.

o Experimental design: Use widely accepted standards for biological replication and statistical analysis; validate genotype–phenotype associations across environments or populations when feasible.

This Topic advances SDG 2 (Zero Hunger) through resilient, productive crops; SDG 13 (Climate Action) by addressing adaptation to climatic stressors; and SDG 15 (Life on Land) by leveraging wild relatives, biodiversity, and plant–symbiont interactions that support ecosystem services.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

  • Brief Research Report
  • Data Report
  • Editorial
  • FAIR² Data
  • General Commentary
  • Hypothesis and Theory
  • Methods
  • Mini Review
  • Opinion

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

  • Brief Research Report
  • Data Report
  • Editorial
  • FAIR² Data
  • General Commentary
  • Hypothesis and Theory
  • Methods
  • Mini Review
  • Opinion
  • Original Research
  • Perspective
  • Policy and Practice Reviews
  • Review
  • Systematic Review
  • Technology and Code

Keywords: Pangenomics; Genetic diversity; Genome editing; CRISPR; Artificial intelligence (AI); Machine learning (ML); Climate-resilient crops; Multi-omics; Breeding; Phytoecosystem; Metagenomics; Plant–microbe interactions

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Topic editors

Frequently asked questions

  • Frontiers' Research Topics are collaborative hubs built around an emerging theme.Defined, managed, and led by renowned researchers, they bring communities together around a shared area of interest to stimulate collaboration and innovation.

    Unlike section journals, which serve established specialty communities, Research Topics are pioneer hubs, responding to the evolving scientific landscape and catering to new communities.

  • The goal of Frontiers' publishing program is to empower research communities to actively steer the course of scientific publishing. Our program was implemented as a three-part unit with fixed field journals, flexible specialty sections, and dynamically emerging Research Topics, connecting communities of different sizes and maturity.

    Research Topics originate from the scientific community. Many of our Research Topics are suggested by existing editorial board members who have identified critical challenges or areas of interest in their field.

  • As an editor, Research Topics will help you build your journal, as well as your community, around emerging, cutting-edge research. As research trailblazers, Research Topics attract high-quality submissions from leading experts all over the world.

    A thriving Research Topic can potentially evolve into a new specialty section if there is sustained interest and a growing community around it.

  • Each Research Topic must be approved by the specialty chief editor, and it falls under the editorial oversight of our editorial boards, supported by our in-house research integrity team. The same standards and rigorous peer review processes apply to articles published as part of a Research Topic as for any other article we publish.

    In 2023, 80% of the Research Topics we published were edited or co-edited by our editorial board members, who are already familiar with their journal's scope, ethos, and publishing model. All other topics are guest edited by leaders in their field, each vetted and formally approved by the specialty chief editor.

  • Publishing your article within a Research Topic with other related articles increases its discoverability and visibility, which can lead to more views, downloads, and citations. Research Topics grow dynamically as more published articles are added, causing frequent revisiting, and further visibility.

    As Research Topics are multidisciplinary, they are cross-listed in several fields and section journals – increasing your reach even more and giving you the chance to expand your network and collaborate with researchers in different fields, all focusing on expanding knowledge around the same important topic.

    Our larger Research Topics are also converted into ebooks and receive social media promotion from our digital marketing team.

     

  • Frontiers offers multiple article types, but it will depend on the field and section journals in which the Research Topic will be featured. The available article types for a Research Topic will appear in the drop-down menu during the submission process.

    Check available article types here 

  • Yes, we would love to hear your ideas for a topic. Most of our Research Topics are community-led and suggested by researchers in the field. Our in-house editorial team will contact you to talk about your idea and whether you’d like to edit the topic. If you’re an early-stage researcher, we will offer you the opportunity to coordinate your topic, with the support of a senior researcher as the topic editor. 

    Suggest your topic here 

  • A team of guest editors (called topic editors) lead their Research Topic. This editorial team oversees the entire process, from the initial topic proposal to calls for participation, the peer review, and final publications.

    The team may also include topic coordinators, who help the topic editors send calls for participation, liaise with topic editors on abstracts, and support contributing authors. In some cases, they can also be assigned as reviewers.

  • As a topic editor (TE), you will take the lead on all editorial decisions for the Research Topic, starting with defining its scope. This allows you to curate research around a topic that interests you, bring together different perspectives from leading researchers across different fields and shape the future of your field. 

     

    You will choose your team of co-editors, curate a list of potential authors, send calls for participation and oversee the peer review process, accepting or recommending rejection for each manuscript submitted.

  • As a topic editor, you're supported at every stage by our in-house team. You will be assigned a single point of contact to help you on both editorial and technical matters. Your topic is managed through our user-friendly online platform, and the peer review process is supported by our industry-first AI review assistant (AIRA).

  • If you’re an early-stage researcher, we will offer you the opportunity to coordinate your topic, with the support of a senior researcher as the topic editor. This provides you with valuable editorial experience, improving your ability to critically evaluate research articles and enhancing your understanding of the quality standards and requirements for scientific publishing, as well as the opportunity to discover new research in your field, and expand your professional network.

  • Yes, certificates can be issued on request. We are happy to provide a certificate for your contribution to editing a successful Research Topic.

  • Research Topics thrive on collaboration and their multi-disciplinary approach around emerging, cutting-edge themes, attract leading researchers from all over the world.

  • As a topic editor, you can set the timeline for your Research Topic, and we will work with you at your pace. Typically, Research Topics are online and open for submissions within a few weeks and remain open for participation for 6 – 12 months. Individual articles within a Research Topic are published as soon as they are ready.

    Find out more about our Research Topics

  • Our fee support program ensures that all articles that pass peer review, including those published in Research Topics, can benefit from open access – regardless of the author's field or funding situation.

    Authors and institutions with insufficient funding can apply for a discount on their publishing fees. A fee support application form is available on our website.

  • In line with our mission to promote healthy lives on a healthy planet, we do not provide printed materials. All our articles and ebooks are available under a CC-BY license, so you can share and print copies.

     

Manuscripts can be submitted to this Research Topic via the main journal or any other participating journal.

Submit your idea

You will be redirected to our submission process.

Submit your manuscript summarySubmit your manuscript

Impact

  • 79Topic views
View impact

Share on WeChat

Scan with WeChat to share this article