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Advances in Multi-Omics for Functional Genomics Studies and Molecular Breeding

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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: 30 June 2025 | Viewed by 8525

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Dr. Chen Chen

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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 Issue Information

Dear Colleagues,

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

Dr. Chen Chen
Guest Editor

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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 (9 papers)

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Research

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16 pages, 5709 KiB

Open AccessArticle

Metabolomics and Transcriptomics Jointly Explore the Mechanism of Pod Color Variation in Purple Pod Pea

by Xiaojuan Zhong, Mei Yang, Xiaoyan Zhang, Yuanfang Fan, Xianshu Wang and Chao Xiang

Curr. Issues Mol. Biol. 2025, 47(2), 94; https://doi.org/10.3390/cimb47020094 (registering DOI) - 1 Feb 2025

Viewed by 178

Abstract

Although the pod color was one of the seven characteristics Mendel studied in peas, the mechanism of color variation in peas with purple pods has not been reported. This study systemically analyzed the difference between two pea accessions with green pods (GPs) and purple pods (PPs) at two pod developmental stages from the metabolome and transcriptome levels, aiming to preliminarily explore the mechanism and of color variation in PPs and screen out the candidate genes. A total of 180 differentially accumulated metabolites (DAMs) belonged to seven flavonoid subgroups and 23 flavonoid-related differentially expressed genes (DEGs) were identified from the analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, respectively. Among the 180 flavonoid metabolites, ten anthocyanin compounds, which were the principal pigments in PPs and might be the major reason for the purple color formation, were significantly up-accumulated in both of the different pod development stages of PPs. A transcriptome analysis revealed that eight genes encoding enzymes (C4H, CHI, F3H, F3’H, F3’5’H, DFR, ANS, and FLS) involved in the flavonoid synthesis pathway were significantly upregulated in PPs and finally resulted in the significant accumulation of flavonoid and anthocyanin metabolites. The joint analysis of two omics and a weighted gene co-expression network analysis (WGCNA) also screened out that the WD-40 protein-encoding gene, one WRKY and three MYB transcription factor genes exhibited significant upregulation in PPs, and highly correlated with several structural genes in flavonoid synthesis pathways, indicating that these genes are involved in the regulation of pod color formation in PPs. Overall, the results of this study first explored the mechanism underlying the purple color variation between PPs and GPs, and then preliminarily screened out some candidate genes responsible for the pod color formation in PPs. Full article

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

6 pages, 1377 KiB

Open AccessCommunication

The First Complete Chloroplast Genome Sequence of Secale strictum subsp. africanum Stapf (Poaceae), the Putative Ancestor of the Genus Secale

by Lidia Skuza, Piotr Androsiuk, Romain Gastineau, Magdalena Achrem, Łukasz Paukszto and Jan Paweł Jastrzębski

Curr. Issues Mol. Biol. 2025, 47(1), 64; https://doi.org/10.3390/cimb47010064 - 17 Jan 2025

Viewed by 725

Abstract

Secale strictum ssp. africanum (synonym Secale africanum), a putative ancestor of the genus Secale, has been classified within Secale strictum, although recent phylogenetic studies suggest that it represents a distinct species. This study reports the first complete chloroplast genome of S. africanum, highlighting its structure, genetic composition, and phylogenetic relationships within Secale and related Triticiceae species. Phylogeny reconstruction based on the maximum-likelihood method reveals notable genetic similarity between S. strictum and S. africanum, supporting their genetic and phylogenetic distinction. Here, we assembled the complete, annotated chloroplast genome sequence of Secale strictum ssp. africanum. The genome is 137,068 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number OQ700974. This work sheds light on the evolutionary history of Secale and contributes to our understanding of chloroplast genomics in cereal ancestors, with potential applications in improving cereal crop resilience, advancing breeding strategies, and informing conservation efforts for genetic diversity. Full article

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

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19 pages, 4185 KiB

Open AccessArticle

Reverse Mutations in Pigmentation Induced by Sodium Azide in the IR64 Rice Variety

by Hsian-Jun Chen, Anuchart Sawasdee, Yu-Ling Lin, Min-Yu Chiang, Hsin-Yi Chang, Wen-Hsiung Li and Chang-Sheng Wang

Curr. Issues Mol. Biol. 2024, 46(12), 13328-13346; https://doi.org/10.3390/cimb46120795 - 22 Nov 2024

Viewed by 686

Abstract

Pigmentation in rice is due mainly to the accumulation of anthocyanins. Five color mutant lines, AZ1701, AZ1702, AZ1711, AZ1714, and AZ1715, derived from the sodium azide mutagenesis on the non-pigmented IR64 variety, were applied to study inheritance modes and genes for pigmentation. The mutant line AZ1711, when crossed with IR64, displays pigmentation in various tissues, exhibiting a 3:1 pigmented to non-pigmented ratio in the F₂ progeny, indicating a single dominant locus controlling pigmentation. Eighty-four simple sequence repeat (SSR) markers were applied to map the pigment gene using 92 F₂ individuals. RM6773, RM5754, RM253, and RM2615 markers are found to be linked to the color phenotype. RM253 explains 78% of the phenotypic variation, implying linkage to the pigmentation gene(s). Three candidate genes, OsC1 (MYB), bHLH, and 3GT, as anthocyanin biosynthesis-related genes, were identified within a 0.83 Mb region tightly linked to RM253. PCR cloning and sequencing revealed 10 bp and 72 bp insertions in the OsC1 and 3GT genes, respectively, restoring pigmentation as in wild rice. The 72 bp insertion is highly homologous to a sequence of Ty1-Copia retrotransposon and shows a particular secondary structure, suggesting that it was derived from the transposition of Ty1-Copia in the IR64 genome. Full article

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

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17 pages, 5639 KiB

Open AccessArticle

Comprehensive Transcriptomic and Physiological Insights into the Response of Root Growth Dynamics During the Germination of Diverse Sesame Varieties to Heat Stress

by Xiaoyu Su, Chunming Li, Yongliang Yu, Lei Li, Lina Wang, Dandan Lu, Yulong Zhao, Yao Sun, Zhengwei Tan and Huizhen Liang

Curr. Issues Mol. Biol. 2024, 46(12), 13311-13327; https://doi.org/10.3390/cimb46120794 - 22 Nov 2024

Viewed by 668

Abstract

Heat stress constitutes a serious threat to sesame (Sesamum indicum L.). Root development during seed germination plays an essential role in plant growth and development. Nevertheless, the regulatory mechanisms underlying heat stress remain poorly understood. In this study, two sesame varieties differing in leaf heat tolerance (Zheng Taizhi 3 (heat-tolerant) and SP19 (heat-sensitive)) have been employed to investigate the impact of heat stress on root growth during germination. The results showed that heat stress significantly reduced the radicle length by 35.71% and 67.02% in Zheng Taizhi 3 and SP19, respectively, while germination rates remained unchanged. In addition, heat stress induced oxidative stress, as evidenced by increased reactive oxygen species (ROS) production, malondialdehyde (MDA) content, and reduced indole-3-acetic acid (IAA) content, accompanied by enhanced antioxidant enzyme activities, including those of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the abscisic acid (ABA) content significantly increased in both varieties. However, the oxidation resistance in the roots of Zheng Taizhi 3 was enhanced compared to that of SP19 under heat stress, while IAA production was maintained and ABA content was reduced. A comparative transcriptome analysis identified 6164 and 6933 differentially expressed genes (DEGs) in Zheng Taizhi 3 and SP19, respectively, with 4346 overlapping DEGs. These DEGs included those related to stress tolerance, such as heat-shock proteins (HSPs), the antioxidant defense system, hormone signal transduction, and the biosynthetic pathway of phenylpropanoid. These findings provide insights into the physiological and molecular mechanisms underlying the adaptation of sesame to heat stress, which could inform breeding strategies for developing heat-tolerant sesame varieties. Full article

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

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12 pages, 2555 KiB

Open AccessArticle

Development of Yein-Early, a Unique Fruit-Color and Leaf-Shape Mutant of Citrus unshiu, and Its Specific Selection Marker

by Jung-Gwon Ko, Chang-Ho Eun and In-Jung Kim

Curr. Issues Mol. Biol. 2024, 46(9), 10606-10617; https://doi.org/10.3390/cimb46090628 - 21 Sep 2024

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Abstract

Citrus unshiu Marc. cv. Miyagawa-wase is one of the most widely cultivated citrus varieties on Jeju Island in Republic of Korea. Mutation breeding is a useful tool for inducing genetic diversity by causing genomic mutations in a short period of time. We previously conducted mutation breeding using gamma irradiation to develop new varieties of C. unshiu. Here, we describe one of these varieties, Yein-early, which has a redder peel, greater hardness, and higher sugar content compared with the wild type (WT). Yein-early leaves also showed a unique phenotype compared with the WT, characterized by longer longitudinal length, shorter transverse length, stronger curling, and longer petiole length. Genome resequencing of Yein-early and the WT uncovered significant single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). These variations were crucial in identifying molecular markers unique to Yein-early. In addition, we developed an allele-specific PCR marker specifically targeting a homozygous SNP in Yein-early that distinguishes it from the WT and other citrus varieties. This study contributes to the understanding of pigment synthesis in fruits and provides a valuable tool for selection of the novel Yein-early variety in citrus breeding programs. Full article

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

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16 pages, 6210 KiB

Open AccessArticle

Transcriptomic and Metabolic Analysis Reveals Genes and Pathways Associated with Flesh Pigmentation in Potato (Solanum tuberosum) Tubers

by Man Li, Yuting Xiong, Xueying Yang, Yuliang Gao and Kuihua Li

Curr. Issues Mol. Biol. 2024, 46(9), 10335-10350; https://doi.org/10.3390/cimb46090615 - 17 Sep 2024

Viewed by 886

Abstract

Anthocyanins, flavonoid pigments, are responsible for the purple and red hues in potato tubers. This study analyzed tubers from four potato cultivars—red RR, purple HJG, yellow QS9, and white JZS8—to elucidate the genetic mechanisms underlying tuber pigmentation. Our transcriptomic analysis identified over 2400 differentially expressed genes between these varieties. Notably, genes within the flavonoid biosynthesis pathway were enriched in HJG and RR compared to the non-pigmented JZS8, correlating with their higher levels of anthocyanin precursors and related substances. Hierarchical clustering revealed inverse expression patterns for the key genes involved in anthocyanin metabolism between pigmented and non-pigmented varieties. Among these, several MYB transcription factors displayed strong co-expression with anthocyanin biosynthetic genes, suggesting a regulatory role. Specifically, the expression of 16 MYB genes was validated using qRT-PCR to be markedly higher in pigmented HJG and RR versus JZS8, suggesting that these MYB genes might be involved in tuber pigmentation. This study comprehensively analyzed the transcriptome of diverse potato cultivars, highlighting specific genes and metabolic pathways involved in tuber pigmentation. These findings provide potential molecular targets for breeding programs focused on enhancing tuber color. Full article

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

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13 pages, 1549 KiB

Open AccessArticle

De Novo Transcriptome Assembly of Cedar (Cedrela odorata L.) and Differential Gene Expression Involved in Herbivore Resistance

by Luis Felipe Guzmán, Bibiana Tirado, Carlos Iván Cruz-Cárdenas, Edith Rojas-Anaya and Marco Aurelio Aragón-Magadán

Curr. Issues Mol. Biol. 2024, 46(8), 8794-8806; https://doi.org/10.3390/cimb46080520 - 14 Aug 2024

Viewed by 1507

Abstract

Timber trees are targets of herbivorous attacks. The identification of genes associated with pest resistance can be accomplished through differential expression analysis using transcriptomes. We reported the de novo assembly of cedar (Cedrela odorata L.) transcriptome and the differential expression of genes involved in herbivore resistance. The assembly and annotation of the transcriptome were obtained using RNAseq from healthy cedar plants and those infested with Chrysobothris yucatanensis. A total of 325.6 million reads were obtained, and 127,031 (97.47%) sequences were successfully assembled. A total of 220 herbivory-related genes were detected, of which 170 genes were annotated using GO terms, and 161 genes with 245 functions were identified—165, 75, and 5 were molecular functions, biological processes, and cellular components, respectively. To protect against herbivorous infestation, trees produce toxins and volatile compounds which are modulated by signaling pathways and gene expression related to molecular functions and biological processes. The limited number of genes identified as cellular components suggests that there are minimal alterations in cellular structure in response to borer attack. The chitin recognition protein, jasmonate ZIM-domain (JAZ) motifs, and response regulator receiver domain were found to be overexpressed, whereas the terpene synthase, cytochrome P450, and protein kinase domain gene families were underexpressed. This is the first report of a cedar transcriptome focusing on genes that are overexpressed in healthy plants and underexpressed in infested plants. This method may be a viable option for identifying genes associated with herbivore resistance. Full article

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

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11 pages, 4953 KiB

Open AccessArticle

Identification of NAC Transcription Factors in Suaeda glauca and Their Responses to Salt Stress

by Xujun Fu, Longmin Zhu, Xiaomin Yu, Qinghua Yang, Fengjie Yuan and Hangxia Jin

Curr. Issues Mol. Biol. 2024, 46(8), 8741-8751; https://doi.org/10.3390/cimb46080516 - 10 Aug 2024

Viewed by 930

Abstract

NAC (NAM/ATAF1/2/CUC2) transcription factors regulate plant growth and development and stress responses. Because NAC transcription factors are known to play important roles in the regulation of salt tolerance in many plants, we aimed to explore their roles in the halophyte Suaeda glauca. Based on transcriptome sequencing data, we identified 25 NAC transcription factor gene family members. In a phylogenetic tree analysis with Arabidopsis thaliana NAC transcription factors, the SgNACs were divided into 10 groups. The physicochemical properties and conserved domains of the putative proteins, as well as the transcript profiles of their encoding genes, were determined for the 25 SgNAC genes using bioinformatic methods. Most of the S. glauca NAC genes were upregulated to some extent after 24 h of salt stress, suggesting that they play an important role in regulating the salt tolerance of S. glauca. These findings lay the foundation for further research on the functions and mechanisms of the NAC gene family in S. glauca. Full article

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

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13 pages, 751 KiB

Open AccessReview

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice

by Jian Song, Liqun Tang, Yongtao Cui, Honghuan Fan, Xueqiang Zhen and Jianjun Wang

Curr. Issues Mol. Biol. 2024, 46(9), 10299-10311; https://doi.org/10.3390/cimb46090613 - 16 Sep 2024

Viewed by 1559

Abstract

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation. Full article

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

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