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

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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 October 2026 | Viewed by 6212

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Dr. Chen Chen

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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
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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

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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 250 words) can be sent to the Editorial Office for assessment.

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.

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Keywords

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

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Published Papers (7 papers)

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25 pages, 15185 KB

Open AccessArticle

Integrated Metabolomics and Transcriptomics Analysis Reveals the Biosynthetic Mechanism of Isoquinoline Alkaloids in Different Tissues of Hypecoum erectum L.

by Sainan Wang, Yan Du and Meiqing Yang

Curr. Issues Mol. Biol. 2026, 48(3), 309; https://doi.org/10.3390/cimb48030309 - 13 Mar 2026

Viewed by 555

Abstract

Hypecoum erectum L. is a medicinal plant known for its high content of isoquinoline alkaloids (IQAs), a class of compounds with diverse pharmacological activities. To elucidate the biosynthetic mechanisms and tissue-specific accumulation of IQAs, we integrated HPLC-MS/MS-based metabolomic analysis with RNA sequencing (RNA-seq) transcriptomic profiling across the roots, stems, and leaves of H. erectum. Metabolomic analysis identified twenty-six IQAs as differentially accumulated metabolites (DAMs) among the three tissues, while transcriptomic analysis revealed twenty-two categories of differentially expressed genes (DEGs) involved in IQA biosynthesis. KEGG pathway enrichment analysis demonstrated that nine DAMs and twenty categories of DEGs were co-enriched in the IQA biosynthetic pathway of Hypecoum erectum. Notably, seven key DAMs—Stylopine, Protopine, Magnoflorine, Corydaline, Tetrahydropalmatine, Sanguinarine, and Palmatine—preferentially accumulated in the root, concomitant with the elevated expression of eleven root-specific DEGs, including GOT1, CYP719A14, SMT, CYP719A1_2_3_13, PSOMT1, E2.1.1.116, CYP80B1, E2.1.1.128, NCS, ASP5, and BBE1. Gene–metabolite correlation network analysis further identified nine DAMs and fifteen DEGs closely associated with IQA biosynthesis, highlighting key enzymatic regulators of alkaloid accumulation. Additionally, several transcription factor (TF) families, including bHLH, NAC, and ERF families, were predicted to participate in the transcriptional regulation of IQA-related genes. Collectively, these findings demonstrate that roots are the primary site of IQA biosynthesis in H. erectum and provide a molecular framework for understanding the regulation and utilization of its medicinally active components. Full article

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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20 pages, 21135 KB

Open AccessArticle

Comprehensive Analysis of the AP2/ERF Superfamily Identifies Key Genes Related to Various Stress Responses in Olive Tree (Olea europaea L.)

by Erli Niu, Song Gao, Mengyun Ren, Wei Wang, Qian Zhao and Ying Fu

Curr. Issues Mol. Biol. 2026, 48(2), 183; https://doi.org/10.3390/cimb48020183 - 5 Feb 2026

Viewed by 633

Abstract

The AP2/ERF superfamily is a key class of transcription factors involved in plant responses to various stresses. As an ancient species, the olive tree (Olea europaea L.) exhibits considerable stress tolerance and wide adaptability. In this study, we identified 348 AP2/ERF genes in the cultivated olive variety ‘Arbequina’ at the whole-genome level. According to protein sequence alignments and phylogenetic analyses via the Maximum Likelihood method, these genes were classified into four major families: AP2, ERF/DREB, RAV, and Soloist. The ERF/DREB family was further divided into DREB and ERF subfamilies, each encompassing six groups (A1–A6 and B1–B6), with the ERF subfamily being the largest. Members of each group exhibited relatively consistent gene structures and domain/motif compositions of their encoded proteins; however, the distribution of cis-elements and expression patterns varied. Each AP2/ERF gene contained 12 light-responsive, three MeJA-responsive, three ABA-responsive, two anaerobic induction, and one MYB binding site on average. With the threshold of p value < 0.5, control TPM > 0, and |log₂(fold change)| > 0, 50 candidate genes were simultaneously up-regulated (30) or down-regulated (20) under four stress treatments (acid–aluminum, cold, disease, and wound), among which nine showed potential protein–protein interactions. This study provides a comprehensive genomic characterization of the AP2/ERF family in olive and identifies key candidate stress-responsive genes, establishing a foundation for future functional studies on the molecular mechanisms of stress adaptation in the olive tree. Full article

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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16 pages, 2091 KB

Open AccessArticle

Genetic Variation in the Main Cultivar Collection of Castanea henryi Revealed by Genome Resequencing

by Yifan Wang, Xueting Yuan, Jinhui Yang, Xibing Jiang, Shipin Chen, Hui Chen and Yu Li

Curr. Issues Mol. Biol. 2026, 48(2), 173; https://doi.org/10.3390/cimb48020173 - 3 Feb 2026

Cited by 1 | Viewed by 514

Abstract

Castanea henryi is an important economic tree species in China. Its nutrient-rich nuts play a key role in raising farmers’ income in mountainous areas, promoting forestry industry development, and maintaining ecological balance, thereby providing significant economic and ecological value. To systematically elucidate the genetic characteristics of major C. henryi cultivars in China, this study conducted phenotypic trait measurements on 42 cultivars collected from Taining and Jian’ou in Fujian Province. Combined with whole-genome resequencing technology and using the C. henryi genome as a reference, systematic analyses were carried out. The results indicated that the Jian’ou group (HJO) generally exhibited superior performance in key fruit phenotypic traits compared to the Taining group (HTNC), with greater phenotypic diversity observed within the HJO group. Clustering analysis of phenotypic traits further revealed a cross-geographic convergent clustering pattern among the 42 C. henryi cultivars. Further analysis revealed that the overall genetic diversity of the 42 C. henryi cultivars was relatively low (observed heterozygosity: HJO = 0.0275, HTNC = 0.0194). Notably, parameters such as heterozygosity, minor allele frequency, nucleotide polymorphism, and polymorphic information content were slightly higher in the Jian’ou group compared to the Taining group. Divergent selection signal analysis (Fst top 5%) identified 3129 genomic regions under divergent selection. Genes within these regions showed homology to 1205 Arabidopsis thaliana genes, reflecting adaptive divergence driven by differential historical selection pressures between the two groups. Population genetic structure analysis indicated that the two regional groups exhibit high genetic similarity and low differentiation. This study reveals low genetic diversity and high genetic background homogeneity among C. henryi cultivars, findings that could inform the design of future breeding strategies. Full article

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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20 pages, 5695 KB

Open AccessArticle

Integrated BSA-Seq and WGCNA Analyses Reveal Candidate Genes Associated with Winter Bud Dormancy Maintenance in Fruit Mulberry (Morus spp.)

by Bing Sun, Zhaoxia Dong, Feng Zhang, Zhixian Zhu, Cheng Zhang and Cui Yu

Curr. Issues Mol. Biol. 2026, 48(1), 38; https://doi.org/10.3390/cimb48010038 - 27 Dec 2025

Viewed by 485

Abstract

The excessively concentrated ripening period of mulberries causes seasonal surplus. Fruit mulberry (Morus spp.) exhibits the unique trait of “simultaneous flowering and leaf flushing”, rendering budburst timing closely correlated with fruit ripening time. Thus, deciphering the molecular mechanism underlying winter bud dormancy maintenance in fruit mulberry is urgently needed. Herein, an F₁ hybrid population comprising 337 individuals, derived from Morus wittiorum (♀) and ‘322’ (♂), was utilized as research material. Through Bulked Segregant Analysis Sequencing (BSA-Seq), we successfully mapped a dormancy-associated QTL interval designated as LB (Late Burst), spanning 9,990,001–11,990,000 bp on Chromosome 13. Integrating Weighted Gene Co-expression Network Analysis (WGCNA) results, MaSVP was identified as a candidate gene within this interval. Virus-induced gene silencing (VIGS) of MaSVP in winter buds of Morus wittiorum significantly accelerated budburst compared to the control, demonstrating that MaSVP represses winter bud dormancy release and plays a crucial role in regulating dormancy maintenance in fruit mulberry. Dynamic expression profiling of dormancy-related genes revealed that the transcript levels of MaSVP, MaSAPK3, MaCASL2, and MaPYR8 were significantly downregulated (Tukey’s test, p < 0.05) as budburst approached, whereas those of MaFT and MaGA20ox1-D were significantly upregulated (Tukey’s test, p < 0.05). These results indicate that winter bud dormancy maintenance in Morus wittiorum is associated with abscisic acid (ABA) and gibberellin (GA) metabolism. Collectively, this study provides critical insights into the biological basis of winter bud dormancy maintenance in fruit mulberry and offers valuable genetic resources for breeding late-maturing cultivars. Full article

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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19 pages, 2455 KB

Open AccessArticle

Genetic Trends in General Combining Ability for Maize Yield-Related Traits in Northeast China

by Haochen Wang, Xiaocong Zhang, Jianfeng Weng, Mingshun Li, Zhuanfang Hao, Degui Zhang, Hongjun Yong, Jienan Han, Zhiqiang Zhou and Xinhai Li

Curr. Issues Mol. Biol. 2025, 47(11), 877; https://doi.org/10.3390/cimb47110877 - 23 Oct 2025

Viewed by 1006

Abstract

Maize (Zea mays L.) is the most extensively cultivated food crop in China, and current studies on maize general combining ability (GCA) focus primarily on the genetic basis of traits. However, the dynamic trends and underlying genetic loci associated with GCA for yield-related traits during breeding remain underexplored. This study was designed to investigate the changing trends of the general combining ability (GCA) and the frequency of elite alleles among 218 major maize inbred lines from Northeast China, spanning the 1970s to the 2010s. PH6WC and PH4CV were used as testers to develop 436 hybrid combinations via the North Carolina design II (NCII) method, and these combinations were evaluated across three environments. We further analyzed the combining ability (particularly the GCA) of 16 yield-related traits and their dynamic trends during breeding, grouped into three age periods (AGE1: 1960s–1970s; AGE2: 1980s–1990s; AGE3: 2000s–2010s). We also screened for genetic loci associated with the GCA effects of these traits. Results show that breeding selection significantly affected the GCA of six yield-related traits (ear length (EL), tassel branch number (TBN), tassel main axis length (TL), kernel length (KL), stem diameter (SDR), and hundred kernel weight (HKW)). Specifically, the mean TBN_GCA value decreased from 2.51 in AGE1 to −1.28 in AGE3, and the mean HKW_GCA increased from −1.58 in AGE1 to 0.36 in AGE3. Yield per plant GCA (YPP_GCA) was positively correlated with the GCA values of EL, ear diameter (ED), kernel row number (KRN), kernel number per row (KNPR), and HKW. Association analysis identified 38 single nucleotide polymorphisms (SNP_S) related to GCA. The T/T alleles for TBN were absent in AGE1, emerged in AGE2 (1980s–1990s), and persisted in AGE3—consistent with the decreasing trend of TBN_GCA from AGE1 to AGE3. For HKW, the A/A alleles not only exhibited higher GCA (effectively improving the HKW_GCA of inbred lines) but also showed an 11% increase in allelic frequency from AGE1 to AGE3. Taken together, these results suggest that the accumulation of elite alleles is the primary factor driving the GCA improvement during maize breeding in Northeast China. Full article

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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28 pages, 4640 KB

Open AccessArticle

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

Cited by 2 | Viewed by 1153

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 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

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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18 pages, 3893 KB

Open AccessArticle

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

Cited by 1 | Viewed by 1285

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 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

(This article belongs to the Special Issue Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding, 2nd Edition)

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