cimb-logo

Journal Browser

Journal Browser

Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 217

Special Issue Editor


E-Mail Website
Guest Editor
Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No.17 Cuihua South Road, Xi’an 710061, China
Interests: genome; biotechnology; molecular biology; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce a Special Issue on ‘Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition’ that will be published in the current Special Issue of Molecular Biology. This Special Issue aims to provide a comprehensive overview of recent advancements in the utilization of multi-omics in non-model plant functional genomics, including the molecular mechanism of plant growth, development, secondary metabolism, responses to biotic and abiotic stresses, and interactions with pathogens or beneficial microorganisms. We also focus on applying these functional genes in various improvement studies through molecular breeding.

Plant genes involve various biological processes, including growth, development, defense against pathogens, and response to environmental stressors. The advancement of sequencing technology has greatly facilitated the investigation of the underlying molecular mechanisms of physiological processes. Recently, multi-omics has been extensively utilized to explore the molecular mechanisms in plants, especially in non-model plants. These breakthroughs have also driven the rapid development of molecular breeding, such as gene-edited soybeans and molecularly designed potato varieties.

This Special Issue will address various topics related to functional genomics and their breeding applications, including multi-omics, gene identification and characterization, gene functional analysis, transformation development, and transgenic plant breeding. We welcome original research articles, reviews, and perspectives that address these topics and provide new insights into the molecular mechanisms that underlie non-model plant growth, development, and responses to biotic and abiotic stress.

We encourage submissions from researchers across the globe who are currently employed in plant genomics and welcome contributions that reflect both fundamental and applied research. We aim to assemble cutting-edge research that will promote advancements in our understanding of non-model plant gene functions and pave the way for developing new and improved crops.

We look forward to receiving your submissions and sharing this exciting research collection with our readers.

You can read the publications in the first volumes of this Special Issue here:

https://www.mdpi.com/journal/cimb/special_issues/XIH4R3U60X

Dr. Chen Chen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Current Issues in Molecular Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • sequencing technologies
  • plant genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • epigenomics
  • single-cell sequencing
  • functional genomics
  • transformation methods
  • gene identification

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

28 pages, 4640 KB  
Article
Proteomic Analysis of Low-Temperature Stress Response in Maize (Zea mays L.) at the Seedling Stage
by Tao Yu, Jianguo Zhang, Xuena Ma, Shiliang Cao, Wenyue Li and Gengbin Yang
Curr. Issues Mol. Biol. 2025, 47(9), 784; https://doi.org/10.3390/cimb47090784 - 22 Sep 2025
Abstract
Low temperature severely restricts maize seedling establishment and yield in northern China, but the proteomic basis of low-temperature tolerance in maize remains unclear. This study used TMT-labeled quantitative proteomics combined with data-independent acquisition (DIA) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to analyze dynamic [...] Read more.
Low temperature severely restricts maize seedling establishment and yield in northern China, but the proteomic basis of low-temperature tolerance in maize remains unclear. This study used TMT-labeled quantitative proteomics combined with data-independent acquisition (DIA) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to analyze dynamic proteome changes in two maize inbred lines (low-temperature-tolerant B144 and low-temperature-sensitive Q319) at the three-leaf stage under 5 °C treatment. A total of 4367 non-redundant proteins were identified. For differentially expressed proteins (DEPs, fold change >2.0 or <0.5, ANOVA-adjusted p < 0.05, false discovery rate [FDR] < 0.05), B144 showed exclusive upregulation under stress (6 DEPs at 24 h; 16 DEPs at 48 h), while Q319 exhibited mixed regulation (9 DEPs at 24 h: 6 upregulated, 3 downregulated; 21 DEPs at 48 h: 19 upregulated, 2 downregulated). Functional annotation indicated that ribosomal proteins, oxidoreductases, glycerol-3-phosphate permease, and actin were significantly upregulated in both lines. Pathway enrichment analysis revealed associations with carbohydrate metabolism, amino acid biosynthesis, and secondary metabolite synthesis. Weighted gene co-expression network analysis (WGCNA) identified genotype-specific expression patterns: B144 showed differential expression of proteins related to acetyl-CoA synthetase and fatty acid β-oxidation at 24 h and of proteins related to D-3-phosphoglycerate dehydrogenase at 48 h; Q319 showed differential expression of proteasome-related proteins at 24 h and of proteins related to elongation factor 1α (EF-1α) at 48 h. Venn analysis found no shared DEPs between the two lines at 24 h but four overlapping DEPs at 48 h. These results clarify proteomic differences underlying low-temperature tolerance divergence between maize genotypes and provide candidate targets for molecular breeding of low-temperature-tolerant maize. Full article
Show Figures

Figure 1

18 pages, 3893 KB  
Article
Metabolome and Transcriptome Analyses of the Molecular Mechanism Underlying Light-Induced Anthocyanin Accumulation in Pepper (Capsicum annuum L.) Peel
by Qinqin He, Liming He, Zongqin Feng, Yunyi Xiao, Qiucheng Qiu, Jiefeng Liu, Hanbing Han and Xinmin Huang
Curr. Issues Mol. Biol. 2025, 47(9), 774; https://doi.org/10.3390/cimb47090774 - 18 Sep 2025
Viewed by 134
Abstract
Under light exposure, certain pepper cultivars synthesize large amounts of anthocyanins in their pericarps, with the illuminated areas exhibiting black coloration. However, research on light-induced anthocyanin formation in pepper fruit, particularly the related metabolites and genetic changes, remains limited. To identify the key [...] Read more.
Under light exposure, certain pepper cultivars synthesize large amounts of anthocyanins in their pericarps, with the illuminated areas exhibiting black coloration. However, research on light-induced anthocyanin formation in pepper fruit, particularly the related metabolites and genetic changes, remains limited. To identify the key genes involved in localized anthocyanin synthesis under light conditions, we investigated the black pericarps (light-exposed) and green pericarps of pepper variety MSCJ1 under illumination. Metabolomics analysis identified 579 metabolites in the black and green pepper pericarps, with 50 differentially accumulated metabolites. Petunidin-3-(6″-p-coumaroyl-glucoside) and delphinidin-3-p-coumaroyl-rutinoid accumulation represented the main factor underlying light-induced blackening of the pericarp. RNA-seq identified 121 differentially expressed genes that were significantly enriched in the flavonoid biosynthesis pathway. The genes for phenylalanine ammonia lyase (Capana09g002200, Capna09g002190), cinnamic acid hydroxylase (Capana06g000273), chalcone synthase (Capana05g002274), flavonoid 3-hydroxylase (Capana02g002586), flavonoid 3′-hydroxylase (MSTRG.15987), dihydroflavonol 4-reductase (Capana02g002763), anthocyanin synthase (Capana01g000365), UDP glucosyltransferase (Capana03g000135), and glutathione S-transferase (Capana02g002285) were key genes for anthocyanin synthesis and transport. Transcription factors bHLH (Capana09g001426, Capana09g001427), HSFB3 (Capana05g000086), and TCP4 (Capana07g002142) participated in the regulation of anthocyanin synthesis. These results broaden our understanding of the mechanism of light-induced anthocyanin synthesis in pepper peel. Full article
Show Figures

Figure 1

Back to TopTop