Big Data Mining in Plant Stress Resistance Evolution and Germplasm Innovation

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

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agronomy agronomy	4.1	7.6	2011	17 Days	CHF 2600	Submit
Crops crops	2.1	2.9	2021	22.4 Days	CHF 1200	Submit
Current Issues in Molecular Biology cimb	4.1	5.0	1999	16.3 Days	CHF 2200	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.8 Days	CHF 2900	Submit
Plants plants	4.7	8.5	2012	16.5 Days	CHF 2700	Submit

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Published Papers (3 papers)

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All Agronomy CIMB Crops IJMS Plants

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23 pages, 8398 KB  

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the CsCAMTA Gene Family in Tieguanyin Tea Plants Under Heat Stress

by Zijia Cui, Hua Wu, Zhicheng Yang, Bohao Xu, Fan Jiang, Rien Lai, Lu Han, Ciding Lu, Dandan Li and Kehui Zheng

Curr. Issues Mol. Biol. 2026, 48(6), 597; https://doi.org/10.3390/cimb48060597 - 5 Jun 2026

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Abstract

Tieguanyin (Camellia sinensis cv. Tieguanyin) is an important oolong tea cultivar in China, and heat stress has become a major environmental constraint affecting its growth and productivity. Calmodulin-binding transcription activators (CAMTAs) are important transcription factors involved in calcium/calmodulin-mediated signaling and [...] Read more.

Tieguanyin (Camellia sinensis cv. Tieguanyin) is an important oolong tea cultivar in China, and heat stress has become a major environmental constraint affecting its growth and productivity. Calmodulin-binding transcription activators (CAMTAs) are important transcription factors involved in calcium/calmodulin-mediated signaling and plant responses to environmental stresses. However, systematic knowledge of the CAMTA gene family in Tieguanyin remains limited. In this study, 20 CsCAMTA genes were identified from the Tieguanyin genome and characterized based on their physicochemical properties, phylogenetic relationships, conserved motifs, gene structures, chromosomal distribution, collinearity, promoter cis-acting elements, and functional annotation. The 20 CsCAMTA genes were unevenly distributed across eight chromosomes, and collinearity analysis suggested that segmental duplication may have contributed to the expansion of this gene family. Conserved motif and domain analyses indicated that CsCAMTA proteins retained typical structural features of CAMTA transcription factors, including CG-1, ANKYR, TIG, and CaMBD/IQ-related regions. Promoter analysis showed that CsCAMTA genes harbored multiple cis-acting elements related to hormone responsiveness, stress response, light response, and growth regulation. Furthermore, qRT-PCR analysis of 18 representative CsCAMTA genes under 40 °C heat treatment revealed distinct temporal expression patterns, suggesting that different CsCAMTA members may respond to heat stress at different stages. Several genes, such as CsCAMTA2, CsCAMTA10, and CsCAMTA16, showed marked transcriptional changes and may represent candidate heat-responsive genes in Tieguanyin. These results provide a systematic overview of the CsCAMTA gene family and lay a foundation for further functional studies of heat stress responses in Tieguanyin. Full article

(This article belongs to the Topic Big Data Mining in Plant Stress Resistance Evolution and Germplasm Innovation)

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20 pages, 7357 KB  

Open AccessArticle

Genome-Wide Analysis of the FAR1/FHY3 (FRS) Gene Family and Expression Responses of PbFRS Genes to PEG-Induced Osmotic Stress, Light, and Shade in Phoebe bournei

by Yizhuo Feng, Ronglin Liu, Ruobing Ying, Zekai Ding, Hengfeng Guan, Xinghao Tang, Kehui Zheng, Zhenzhen Zhang and Shijiang Cao

Int. J. Mol. Sci. 2026, 27(11), 5004; https://doi.org/10.3390/ijms27115004 - 1 Jun 2026

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Abstract

Water availability and light conditions are among the most important environmental factors affecting tree growth and development. The FAR1/FHY3 (FRS) gene family consists of transposase-derived transcription factors that are widely involved in light signaling and responses to environmental stresses. [...] Read more.

Water availability and light conditions are among the most important environmental factors affecting tree growth and development. The FAR1/FHY3 (FRS) gene family consists of transposase-derived transcription factors that are widely involved in light signaling and responses to environmental stresses. Although FRS genes have been characterized in several plant species, a comprehensive analysis in P. bournei is still lacking. In this study, we performed the first comprehensive genome-wide analysis of the FRS gene family in P. bournei, including physicochemical characterization, chromosomal localization, phylogenetic analysis, gene structure and conserved motif analysis, protein structure prediction, promoter cis-element analysis, organ/tissue expression profiling, and RT-qPCR analysis under PEG-induced osmotic stress, full-light, and shade treatments. A total of 21 PbFRS genes were identified and found to be unevenly distributed across 11 chromosomes. Phylogenetic analysis, together with Arabidopsis thaliana and Zea mays FRS proteins, clustered the family members into five clades, including one P. bournei-specific clade, suggesting lineage-specific expansion and possible functional diversification. Structural analyses revealed both conserved and divergent features among PbFRS members. Promoter analysis identified diverse cis-acting elements related to light, temperature, hormones, and stress responses, suggesting that PbFRS genes may have diverse regulatory potentials in response to environmental signals. Organ/tissue expression profiling further revealed clear differences in expression patterns among family members. In addition, RT-qPCR analysis showed that several genes, including PbFRS9, PbFRS10, PbFRS12, PbFRS13, PbFRS16, and PbFRS18, exhibited transcriptional responses to PEG-induced osmotic stress, full-light, and shade treatments. These results indicate that these genes may serve as candidates for future functional studies, although their direct roles in stress tolerance require further validation. Overall, these results provide the first systematic overview of the PbFRS gene family and identify transcriptionally responsive candidate genes for future functional studies in P. bournei. Full article

(This article belongs to the Topic Big Data Mining in Plant Stress Resistance Evolution and Germplasm Innovation)

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15 pages, 2761 KB  

Open AccessArticle

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

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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

(This article belongs to the Topic Big Data Mining in Plant Stress Resistance Evolution and Germplasm Innovation)

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