Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower DOI Open Access
Zhihua Wu,

Yan Na Hu,

Rui Hao

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3867 - 3867

Published: April 19, 2025

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating large-scale production of these plants and their derivatives. are exposed a variety internal external factors that interact influence biosynthesis accumulation secondary metabolites. With rapid development omics technologies such genomics, transcriptomics, proteomics, metabolomics, multi-omics become important tools revealing complexity functionality organisms. They conducive further uncovering biological activities metabolites medicinal clarifying molecular mechanisms underlying Also, artificial intelligence (AI) technology accelerates comprehensive utilization high-dimensional datasets offers transformative potential analysis. However, there is currently no systematic review summarizing genomic metabolite plants. Safflower (Carthamus tinctorius L.) has rich diverse bioactive flavonoids, among which Hydroxysafflor yellow A (HSYA) specific safflower emerging medication treating wide range diseases. Hence, progress been made study an excellent example regulation recent years. Here, we on understanding main at level, summarize various types contents, with particular focus flavonoids. This aims provide insight into regulatory from perspective genomics.

Language: Английский

Plant pan-genomics and its applications DOI Creative Commons
Junpeng Shi, Zhixi Tian, Jinsheng Lai

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 168 - 186

Published: Dec. 15, 2022

Language: Английский

Citations

72
The role of pangenomics in orphan crop improvement DOI Creative Commons
Haifei Hu, Junliang Zhao, William J. W. Thomas

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Global food security depends heavily on a few staple crops, while orphan despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes later pangenomes. Recent advances DNA sequencing enabled pangenome construction for several offering more comprehensive understanding genetic diversity. Orphan crop research has now entered pangenomics era applying these pangenomes with advanced selection methods genome editing technologies can transform neglected species into broader agricultural significance. A reference is not enough to harness full variation species. Here, authors review principles, applications improvement, discuss possible ways support pangenomics-driven molecular breeding.

Language: Английский

Citations

3
Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops DOI Open Access
Miguel Ángel Villalobos-López, Analilia Arroyo-Becerra,

Anareli Quintero-Jiménez

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(19), P. 12053 - 12053

Published: Oct. 10, 2022

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops not tolerant climatic environments. aim near future, a world with hunger an population, breed and/or engineer tolerate abiotic stress higher yield. Some crop varieties display certain degree of tolerance, which has been exploited by plant breeders develop thrive under conditions. Moreover, long list genes involved tolerance have identified characterized molecular techniques overexpressed individually transformation experiments. Nevertheless, phenotypes polygenetic traits, current genomic tools dissecting exploit their use accelerating genetic introgression using markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe mechanisms sense adverse conditions examine discuss classic new select improve crops.

Language: Английский

Citations

50
The genomic route to tomato breeding: Past, present, and future DOI Creative Commons

Yan Wang,

Chuanlong Sun, Zhibiao Ye

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2500 - 2514

Published: April 30, 2024

Over the past 10,000 years, tomato species have undergone both unintentional and intentional selection to enhance their favorable traits for human consumption manufacturing. These processes significantly influenced genomes of played a critical role in improving varieties. In this review, we summarize recent advances genome sequencing, explore impact human-driven selection, recapitulate key genes associated with important agronomic breeding. We provide several examples genomics-guided breeding highlight potential resources facilitating improvement. Furthermore, elaborate progress strategies through design present how such efforts can help future enhancements align demands sustainability evolving societies.

Language: Английский

Citations

15
From single- to multi-omics: future research trends in medicinal plants DOI Creative Commons
Lifang Yang, Ye Yang, Luqi Huang

et al.

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Nov. 22, 2022

Abstract Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies medicinal performed to identify molecular markers species functional genes controlling key biological traits, as well understand biosynthetic pathways bioactive regulatory mechanisms environmental responses. Omics technologies applied plants, including taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics mutagenomics. However, because complex regulation network, single usually fail explain specific phenomena. In recent years, reports integrated multi-omics increased. Until now, there few assessments developments upcoming trends in plants. We highlight research summarise typical bioinformatics resources available for analysing datasets, discuss related future directions challenges. This information facilitates further refinement current approaches leads new ideas.

Language: Английский

Citations

32
Artificial Intelligence and Intellectual Property Protection in Indonesia and Japan DOI Creative Commons
Rian Saputra,

Tiara Tiolince,

Iswantoro Iswantoro

et al.

Journal of Human Rights Culture and Legal System, Journal Year: 2023, Volume and Issue: 3(2), P. 210 - 235

Published: May 8, 2023

This research aims to show the impact of artificial intelligence (AI) on fillings patent protection through rights. is normative legal using a comparative approach in Japanese AI system. The results indicate that regulation intellectual property rights Indonesia has not been accommodated Indonesian national However, closest method for its can be performed copyright, but it still shortcomings, where copyright only considered same as ordinary computer software general, which should have significant differences. space Japan patents, provided question contains elements or categories protected patents. right, fact, very complicated and varied Japan.

Language: Английский

Citations

17
Technological Development and Advances for Constructing and Analyzing Plant Pangenomes DOI Creative Commons
Haifei Hu,

Risheng Li,

Junliang Zhao

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(4)

Published: April 1, 2024

Abstract A pangenome captures the genomic diversity for a species, derived from collection of genetic sequences diverse populations. Advances in sequencing technologies have given rise to three primary methods construction and analysis: de novo assembly comparison, reference genome-based iterative assembly, graph-based construction. Each method presents advantages challenges processing varying amounts structures DNA data. With emergence high-quality genome assemblies advanced bioinformatic tools, is emerging as an exploring biological functional implications variations.

Language: Английский

Citations

8
GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa DOI Creative Commons
Michael F. Nagle, Jialin Yuan, Damanpreet Kaur

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(4)

Published: Feb. 7, 2024

Abstract Plant regeneration is an important dimension of plant propagation and a key step in the production transgenic plants. However, capacity varies widely among genotypes species, molecular basis which largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover genetic trait variation plants; however, performance these depends on accuracy scale phenotyping. To enable large-scale GWAS planta callus shoot model tree Populus, we developed phenomics workflow involving semantic segmentation quantify regenerating tissues over time. We found that resulting statistics were highly non-normal distributions, thus employed transformations or permutations avoid violating assumptions linear models used GWAS. report 200 statistically supported quantitative loci (QTLs), with genes encompassing near top QTLs including regulators cell adhesion, stress signaling, hormone signaling pathways, well other diverse functions. Our results encourage hormonal during consider keystone roles stress-related (e.g. jasmonates salicylic acid), addition auxin cytokinin pathways commonly considered. The putative regulatory biological processes identified provide new insights into complexity regeneration, may serve reagents for improving transformation recalcitrant species.

Language: Английский

Citations

7
Plant genome information facilitates plant functional genomics DOI Creative Commons

Judith Jazmín Bernal-Gallardo,

Stefan de Folter

Planta, Journal Year: 2024, Volume and Issue: 259(5)

Published: April 9, 2024

Abstract Main conclusion In this review, we give an overview of plant sequencing efforts and how impacts functional genomics research. Plant genome sequence information greatly facilitates the studies biology, genomics, evolution genomes genes, domestication processes, phylogenetic relationships, among many others. More than two decades have boosted number available sequenced genomes. The first genome, Arabidopsis, was published in year 2000 currently, 4604 from 1482 species been published. Various large initiatives are running, which planning to produce tens thousands near future. on status use different research areas.

Language: Английский

Citations

7
Differences in activity and stability drive transposable element variation in tropical and temperate maize DOI Creative Commons
Shujun Ou, Tyler Collins, Yinjie Qiu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 9, 2022

Abstract Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore extent TE within species, we developed an optimized open-source algorithm, panEDTA, de novo annotate TEs a pan-genome context. We then generated unified annotation for maize derived from 26 reference-quality genomes, which revealed excess 35.1 Mb sequences per tropical relative temperate maize. A small number (n = 216) families, mainly LTR retrotransposons, drive these differences. Evidence methylome, transcriptome, age distribution, and insertional polymorphisms that 64.7% variability was contributed by families were young, less methylated, more expressed maize, while 18.5% driven with removal or loss This study demonstrates use comprehensive pan-TE reveal driving role within-species genomic via their ongoing amplification purging.

Language: Английский

Citations

28