Topic Editors

State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Dr. Shijiang Cao
College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China

Big Data Mining in Plant Stress Resistance Evolution and Germplasm Innovation

Abstract submission deadline
30 October 2026
Manuscript submission deadline
31 December 2026
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844

Topic Information

Dear Colleagues,

This Topic welcomes the submission of interdisciplinary research at the intersection of AI, bioinformatics, big data mining, plant stress biology, evolutionary biology, and genetic breeding. Topics of interest include, but are not limited to, the following:

Development and optimization of AI, machine learning, and deep learning models, as well as advanced bioinformatics workflows, for the integration, mining, and functional interpretation of plant stress-related multi-omics data (including genomics, pan-genomics, transcriptomics, single-cell omics, epigenomics, proteomics, and metabolomics).

Big data-driven dissection of the adaptive evolution mechanisms of plant stress resistance, including natural selection signature analysis, domestication sweep identification, and evolutionary dynamics of stress-responsive gene families in model plants, crops, and forest trees.

Large-scale population genomics studies, including genome-wide association studies (GWASs), genomic selection, expression quantitative trait locus (eQTL) mapping, and pan-genome mining of novel stress-resistant alleles from wild germplasm resources.

Functional validation and in-depth molecular mechanism characterization of key stress-related genes, non-coding RNAs, and regulatory networks identified via big data mining, in response to both abiotic stresses (drought, salinity, extreme temperature, heavy metal toxicity, waterlogging, etc.) and biotic stresses (pathogen infection, pest infestation, etc.).

Innovation and application of big data and AI-enabled precision breeding technologies, including genome design breeding, molecular marker-assisted selection, and genomic prediction, for the development of stress-resilient crop and forest tree germplasms.

Cross-species comparative genomics and evolutionary analysis of plant stress adaptation strategies across herbaceous and woody plant species.

Manuscripts that are purely descriptive, lack innovative algorithm development or in-depth mechanistic insights, and do not align with the core theme of this Topic will not be considered for peer review.

Dr. Yan Cheng
Prof. Dr. Yuling Lin
Dr. Shijiang Cao
Topic Editors

Keywords

  • plant stress resistance
  • adaptive evolution
  • artificial intelligence
  • bioinformatics
  • big data mining
  • molecular regulatory mechanism
  • germplasm innovation
  • genetic breeding
  • multi-omics
  • crop and forest tree improvement

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Agronomy
agronomy
3.4 6.7 2011 17 Days CHF 2600 Submit
Crops
crops
1.9 2.4 2021 22.4 Days CHF 1200 Submit
Current Issues in Molecular Biology
cimb
3.0 3.7 1999 16.3 Days CHF 2200 Submit
International Journal of Molecular Sciences
ijms
4.9 9.0 2000 17.8 Days CHF 2900 Submit
Plants
plants
4.1 7.6 2012 16.5 Days CHF 2700 Submit

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Published Papers (1 paper)

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15 pages, 2761 KB  
Article
Genome-Wide InDel Marker Development and Genetic Diversity Analysis of 52 Tomato Germplasm Accessions
by Chenjiao Huang, Di Ge, Yaxuan Zhang, Zhiye Ge, Yicheng Wu, Qianrong Zhang, Yunxia Zhao and Chonghui Ji
Plants 2026, 15(7), 1118; https://doi.org/10.3390/plants15071118 - 6 Apr 2026
Viewed by 490
Abstract
To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties (‘Micro-Tom’, ‘Moneymaker’, ‘M82’, ‘Heinz 1706’, and ‘LA2093’), a total of 285,796 InDel loci were [...] Read more.
To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties (‘Micro-Tom’, ‘Moneymaker’, ‘M82’, ‘Heinz 1706’, and ‘LA2093’), a total of 285,796 InDel loci were preliminarily identified. Based on these loci, a total of 255 pairs of molecular markers were developed. Subsequently, based on InDel length, polymorphism, and electrophoretic performance, 63 InDel markers with stable amplification, clear polymorphic bands, and coverage across all 12 chromosomes were rigorously selected. These markers were subsequently used to analyze the genetic diversity of 52 tomato germplasm resources. The polymorphism information content (PIC) values of the markers ranged from 0.074 to 0.402, with an average of 0.2804. Cluster analysis based on InDel genotyping data divided the 52 germplasm samples into four distinct groups with significant genetic differentiation, which was validated in conjunction with previously collected phenotypic data from the 52 tomato germplasm resources. Furthermore, a set of core InDel primer combinations (24 pairs) was selected to construct unique DNA fingerprint profiles for each germplasm group. Overall, the InDel markers developed in this study provide an efficient tool for evaluating genetic diversity in tomato germplasm and offer a reliable molecular basis for germplasm identification, heterosis prediction, and marker-assisted breeding, thereby facilitating the development of improved tomato cultivars. Full article
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