Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(4), P. 1466 - 1466

Published: Feb. 10, 2025

The advancement of multi-omics tools has revolutionized the study complex biological systems, providing comprehensive insights into molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify characterize elements that contribute to phenotypic traits. This review delves recent progress in applying approaches elucidate genetic, epigenetic, metabolic networks associated with key plants. We emphasize potential these integrative strategies enhance crop improvement, optimize agricultural practices, promote sustainable environmental management. Furthermore, we explore future prospects field, underscoring importance cutting-edge technological advancements need for interdisciplinary collaboration address ongoing challenges. bridging this aims provide a holistic framework advancing research plant biology agriculture.

Language: Английский

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Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 9, 2025

Abstract Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This addressed here in green foxtail millet ( Setaria viridis ). First, we used RepeatExplorer2 calculate proportion (GP) all repeat types compared GP long terminal (LTR) retroelements against annotated complete incomplete LTR (Ty1/copia Ty3/gypsy) identified by DANTE a whole assembly. We show that DANTE‐identified can comprise ∼0.75% inflorescence poly‐A transcriptome ∼0.24% stem ribo‐depleted transcriptome. In RNA libraries from tissue, both transposons were highly abundant, where they may be taking advantage reduced epigenetic silencing germ line amplify. Typically, there was higher representation than RepeatExplorer2‐identified retroelements, potentially reflecting elements have insufficient genomic copy numbers detected RepeatExplorer2. contrast, for tissues, reverse observed, with retroelements. For repeats, most Ty1/copia Ty3/gypsy families positively correlated their transcript proportion. addition, guanine‐ cytosine‐rich repeats high sequence similarity also abundant transcriptome, these likely represent young are capable amplification due ability evade silencing.

Language: Английский

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Genome-wide identification and comparative evolution of 14–3-3 gene family members in five Brassicaceae species

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 29, 2025

The 14-3-3 proteins are highly conserved regulatory eukaryotic proteins, which crucial in growth, development, and stress responses. However, systematic characterization of the gene family Brassicaceae species their evolutionary relationships have not been comprehensively reported. This study conducted genome-wide identification, structural characteristics, comparative analysis members Arabidopsis thaliana, A. lyrata, pumila, Camelina sativa, Brassica oleracea using genomics. Overall, a total 108 genes, were phylogenetically classified into ε non-ε groups identified five species, with exhibiting more similar exon-intron structures motif patterns. Collinearity revealed that underwent varying degrees expansion following whole-genome duplication (WGD) events. Notably, number between lyrata thaliana remained despite former having approximately 1.66-fold larger genome size. In contrast, pumila C. sativa increased proportionately to size, while distantly related B. oleracea, showed irregular Selection pressure homologs all purifying selection, group experiencing relatively weaker selection. Cloning ApGRF6-2 from indicated protein was localized cell membrane cytoplasm, ectopic overexpression could promote early flowering by upregulating expression floral meristem identity genes. provides comprehensive identification updated sequences, results form basis for further validation functional molecular mechanisms genes plant abiotic responses, as well regulation.

Language: Английский

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Pan-genome identification and expression analysis of the auxin response gene family in potato

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Background The auxin response factor plays an important role in plant growth and development, stress resistance. In this study, the family was identified based on 47 high-quality potato pan-genomes. Results There were no core or private genes among 28 members of pan-gene family, with only one being a near-core gene, while rest non-essential genes. Ka/Ks ratio values showed that gene under positive selection, remaining purifying selection. Structural variations 21 genomes did not significantly affect expression members, nor any significant differences observed. led to changes conserved domains some strains. RNA-seq data analysis response-factor differentially expressed drought relative control conditions; moreover, various differed stress. Further revealed transcription factors involved regulating members. Conclusions Our findings function biological processes potato, provide new theoretical reference for resistance-breeding crop species.

Language: Английский

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Powering up Plant Genetic Research with Genomic Data 2.0

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(9), P. 4052 - 4052

Published: April 25, 2025

Historically, plant genomic research has lagged behind mammalian studies, primarily due to the complexity of genomes and limited resources [...]

Language: Английский

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Next generation breeding in the omics era

Reproduction and Breeding, Journal Year: 2025, Volume and Issue: 5(2), P. 88 - 91

Published: May 9, 2025

Language: Английский

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Genome-Wide Association Studies (GWAS) in Pulses: A Genomic Perspective to Drought

Published: Jan. 1, 2025

Language: Английский

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A Simple and Efficient Protocol to Transform and Regenerate CRISPR-Cas9-Mediated Genome-Edited Tomato Plants

Methods in molecular biology, Journal Year: 2025, Volume and Issue: unknown, P. 213 - 228

Published: Jan. 1, 2025

Language: Английский

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Genomic Selection for Phenotype Prediction in Rice

Published: Jan. 1, 2024

Language: Английский

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