Genome-Wide Identification and Characterization of lncRNAs in sunflower endosperm DOI Creative Commons
Shuai Yu, Zhichao Zhang, Jing Li

et al.

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: Aug. 19, 2022

Abstract Background: Long non-coding RNAs (lncRNAs), as important regulators, play roles in plant growth and development. The expression epigenetic regulation of lncRNAs remain uncharacterized generally seeds, especially the transient endosperm dicotyledons. Results: In this study, we identified 11,840 candidate 12 day-after-pollination sunflower by analyzing RNA-seq data. These were evenly distributed all chromosomes had specific features that distinct from mRNAs including tissue-specificity expression, shorter fewer exons. By GO analysis protein coding genes showing strong correlation with lncRNAs, revealed these potential function many biological processes seed Additionally, genome-wide DNA methylation analyses level at transcription start sites was negatively correlated gene levels lncRNAs. Finally, 36 imprinted 32 maternally expressed four paternally CG CHG context, upstream body regions slightly lower than embryo tissues, which indicated maternal demethylation potentially induce bias endosperm. Conclusion: Our findings not only characterized on a scale development endosperm, but also provide novel insights into parental effects dicotyledonous seeds.

Language: Английский

The genome awakens: transposon-mediated gene regulation DOI
Ileana Tossolini, Regina Mencia, A. Arce

et al.

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

3
CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals – current status, improvements, and perspectives DOI Creative Commons
Sunny Ahmar, Göetz Hensel, Damian Gruszka

et al.

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 69, P. 108248 - 108248

Published: Sept. 2, 2023

Cereal crops, including triticeae species (barley, wheat, rye), as well edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop were developed mainly optimal environmental conditions. Thus, it has become evident that taking into account ongoing climate changes, currently a priority should be given developing new stress-tolerant cultivars. It is necessary enhance accuracy methods time required generate cultivars desired features adapt change keep up world population expansion. The CRISPR/Cas9 system been powerful versatile genome editing tool achieve desirable traits, such high-yielding, stress-tolerant, disease-resistant transgene-free lines in major cereals. Despite recent advances, application faces several challenges, amount develop lines, laboriousness, limited number genotypes may used transformation vitro regeneration. Additionally, through restricted many countries, especially Europe New Zealand, due lack flexibility GMO regulations. This review provides comprehensive update researchers interested improving using gene-editing technologies, CRISPR/Cas9. We will some critical studies on improvements their contributing factors superior technologies.

Language: Английский

Citations

30
The Tomato lncRNA47258-miR319b-TCP Module in Biocontrol Bacteria Sneb821 Induced Plants Resistance to Meloidogyne incognita DOI Creative Commons
Fan Yang, Xiaoxiao Wu, Lijie Chen

et al.

Pathogens, Journal Year: 2025, Volume and Issue: 14(3), P. 256 - 256

Published: March 5, 2025

Long non-coding RNAs (lncRNAs) represent a class of RNAs. In the study Pseudomonas putida Sneb821-induced tomato resistance to Meloidogyne incognita, reverse transcription polymerase chain reaction (RT-PCR) was employed validate 12 lncRNAs in tomato. Among them, lncRNA47258/miR319b/TCP molecular regulatory module likely implicated process against M. incognita. Through application hairy root and virus-induced gene silencing (VIGS) technologies for investigation lncRNA47258, it determined that lncRNA47258 could target TCP (Solyc07g062681.1) modulate metabolic pathway jasmonic acid-related indices, thereby impeding infection Moreover, overexpression using technology demonstrated regulate acid synthesis tomato, consequently obstructing suppressing development Collectively, preliminarily verified be involved incognita

Language: Английский

Citations

1
Harnessing hormone gibberellin knowledge for plant height regulation DOI
Shanshan Wang, Yijun Wang

Plant Cell Reports, Journal Year: 2022, Volume and Issue: 41(10), P. 1945 - 1953

Published: July 20, 2022

Language: Английский

Citations

31
Abiotic stress-induced DNA methylation in transposable elements and their transcripts reveals a multi-layered response in Moso bamboo DOI
Yiqian Ding, Long−Hai Zou, Muthusamy Ramakrishnan

et al.

Industrial Crops and Products, Journal Year: 2024, Volume and Issue: 210, P. 118108 - 118108

Published: Feb. 7, 2024

Language: Английский

Citations

6
A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-l-methionine synthetase DOI Creative Commons
Jiaxing Tian, F.R. Zhang, Guoyu Zhang

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 940 - 957

Published: Feb. 28, 2024

Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding molecular mechanisms regulating because its variable shape and size large inferior ovary. Here, we performed strand-specific transcriptome sequencing on maxima "Rimu") fruits at 6 developmental stages identified 5,425 reliably expressed lncRNAs. Among 332 that were differentially during development, lncRNA MSTRG.44863.1 was as negative regulator development. showed relatively high expression level an obvious period-specific pattern. Transient overexpression silencing significantly increased decreased content 1-aminocyclopropane carboxylic acid (a precursor ethylene) ethylene production, respectively. RNA pull-down microscale thermophoresis assays further revealed can interact with S-adenosyl-L-methionine synthetase (SAMS), enzyme synthesis pathway. Considering negatively regulates these results indicate plays role regulation possibly through interacting SAMS affecting synthesis. Overall, our findings provide rich resource study fruit-related while offering insights into plants.

Language: Английский

Citations

5
Plant long non-coding RNAs: identification and analysis to unveil their physiological functions DOI Creative Commons

Edmundo Domínguez-Rosas,

Miguel Ángel Hernández‐Oñate, Selene L. Fernández-Valverde

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 26, 2023

Eukaryotic genomes encode thousands of RNA molecules; however, only a minimal fraction is translated into proteins. Among the non-coding elements, long RNAs (lncRNAs) play important roles in diverse biological processes. LncRNAs are associated mainly with regulation expression genome; nonetheless, their study has just scratched surface. This somewhat due to lack widespread conservation at sequence level, addition relatively low and highly tissue-specific patterns, which makes exploration challenging, especially plant where few these molecules have been described completely. Recently published high-quality crop plants, along new computational tools, considered promising resources for studying plants. review briefly summarizes characteristics lncRNAs, presence conservation, different protocols find limitations protocols. Likewise, it describes physiological phenomena. We believe that lncRNAs can help design strategies reduce negative effect biotic abiotic stresses on yield plants and, future, create fruits vegetables improved nutritional content, higher amounts compounds positive effects human health, better organoleptic characteristics, longer postharvest shelf life.

Language: Английский

Citations

11
Gene editing of non-coding regulatory DNA and its application in crop improvement DOI

Yu-Hao Chen,

Jun Lu, Yang Xia

et al.

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 74(19), P. 6158 - 6175

Published: Aug. 7, 2023

Abstract The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes generate transgene-free crops. Significant progress been made in editing protein-coding genes; however, studies on non-coding DNA with regulatory roles lags far behind. Non-coding DNAs, including those which can be transcribed into long RNAs (lncRNAs), miRNAs, together cis-regulatory elements (CREs), play crucial regulating plant growth development. Therefore, combination CRISPR/Cas technology great potential novel alleles that affect various agronomic traits crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances DNA, attempts improvement, application tools modulating DNA. Finally, existing problems, possible solutions, future applications gene modern breeding practice are also discussed.

Language: Английский

Citations

11
Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation DOI

Mei Zhou,

Yakun Li, Zhuowei Cheng

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2023, Volume and Issue: 71(43), P. 15895 - 15907

Published: Oct. 20, 2023

Plant height is an important agronomic trait that closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating height. Increasing reports indicate transcriptional regulation major point the GA pathways. Although substantial knowledge has been gained regarding biosynthetic signaling pathways, factors contributing to regulatory mechanisms homeostatically controlling levels remain be elucidated. Here, we provide overview current network involving transcription factors, noncoding RNAs, histone modifications involved We also discuss interaction between GAs other hormones development. Finally, future directions for applying hormone breeding are described.

Language: Английский

Citations

10
MtCIR2 negatively regulates seed germination to salt stress by disrupting metabolisms and signaling of ABA and GAs DOI
Xiaohan Sun, Rui Tian,

Mingui Zhao

et al.

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: 220, P. 109493 - 109493

Published: Jan. 9, 2025

Language: Английский

Citations

0