Seed Biology, Journal Year: 2020, Volume and Issue: 0(0), P. 1 - 15
Published: Jan. 1, 2020
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: June 3, 2024
Abstract Cereal grain size and quality are important agronomic traits in crop production. The development of wheat grains is underpinned by complex regulatory networks. precise spatial temporal coordination diverse cell types essential for the formation functional compartments. To provide comprehensive spatiotemporal information about biological processes developing grain, we performed a transcriptomics study during early stage from 4 to 12 days after pollination. We defined set tissue-specific marker genes discovered that certain or gene families exhibit specific expression patterns over time. Weighted co-expression network motif enrichment analyses identified groups potentially regulating development. embryo surrounding endosperm specifically expressed transcription factor TaABI3-3B negatively regulates size. In Chinese breeding programs, haplotype associated with higher weight was identified, linked altered levels . Data knowledge obtained proposed will pivotal insights into yield improvement serve as genetic future breeding.
Language: Английский
Citations
3
BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)
Published: Feb. 17, 2025
Language: Английский
Citations
0
Physiologia Plantarum, Journal Year: 2025, Volume and Issue: 177(2)
Published: March 1, 2025
Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation one of the most important adaptive strategies in waterlogging-tolerant plants. However, conservation this process remains poorly understood, additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, metabolomic analyses were conducted on wheat seedlings under normal waterlogging conditions. caused growth inhibition physiological damage, as well induced roots. A total 10,346 differentially expressed genes 3,419 differential metabolites identified In addition AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating also revealed role LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) waterlogging. It was that classical pathway mediated by ethylene response, synergy calcium ion reactive oxygen species, deeply conserved both monocots eudicots during 160 million years evolution through co-expression networks cross-species. The newly introduced concept 'Regulatome' supported formation, with proposed model jasmonic acid signalling involved waterlogging, suggesting its usefulness identification function exploration. These findings provide novel insight into regulatory mechanisms breeding approaches for developing cultivars high tolerance.
Language: Английский
Citations
0
Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown
Published: March 26, 2025
Dense planting represents a significant strategy for enhancing soybean yield. However, the shade avoidance response elicited by such density may hinder further yield enhancements. To acquire comprehensive understanding of spatiotemporal responses to shading signals, we segmented treatment into three distinct periods and performed transcriptomic analyses on apical tissues, first internode, hypocotyl, petiole, leaves during these intervals. Enrichment analysis indicated that hormone signalling networks are substantially modulated predominantly involving hormones as auxins, gibberellins, brassinosteroids. Through weighted correlation network motif enrichment analyses, identified several gene groups transcription factors be implicated in soybeans. Furthermore, utilizing transient expression system, validated functions key genes, discovering GmGA20ox, GmUGT73C2, GmWRKY75c involved regulation homoeostasis, thereby reinforcing validity our analytical findings. This study delineates framework avoidance, highlighting clusters essential regulatory genes govern homoeostasis plant architecture. The findings provide critical insights breeding strategies pertinent dense intercropping systems.
Language: Английский
Citations
0
Genome biology, Journal Year: 2025, Volume and Issue: 26(1)
Published: April 11, 2025
Cereal grain size and quality are critical agronomic traits in crop production. Wheat development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments different cell types. Here, we perform a spatial transcriptomics study covering the early stages wheat development, from 4 12 days after pollination. We classify into 10 distinct types identify 192 marker genes associated with them. WGCNA analysis reveals highly expressed exhibit enrichment patterns, significantly influencing filling. Through co-expression motif analyses, specific group may regulate including TaABI3-B1, transcription factor specifically embryo surrounding endosperm, which negatively affects size. This presents comprehensive transcriptional dataset for understanding development. Additionally, it identifies key genetic resources potential applications improving yield.
Language: Английский
Citations
0
BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)
Published: May 10, 2025
Abstract Background Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic metabolomic changes ABA-treated germinating barley ( Hordeum vulgare ) embryos. map ABA-responsive gene expression across embryonic tissues, employed Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied enabled precise localization of six embryo regions, offering insights into tissue-specific patterns that cannot resolved by traditional RNA-seq. Results Transcriptomic analysis indicated ABA acts primarily as a repressor. Gene ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) enrichment analyses linked ABA-inhibited genes energy metabolism, lignin biosynthesis, cell wall organization, photosynthesis, while induced were associated with environmental adaptation phytohormone signaling. Differentially expressed (DEGs) correlated metabolites involved pathways, gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, metabolism. Comparisons developing transcriptomes suggested an ABA-associated signature transcriptomics technique made possible identification ABA-induced transcriptional within distinct tissues. Conclusions Integrating transcriptomics, metabolomics spatial defined modulation phytohormonal crosstalk, activity seeds. The successful use adds novel layer resolution for understanding responses during germination. These findings offer new potential strategies enhancing crop resilience.
Language: Английский
Citations
0
Computational and Structural Biotechnology Journal, Journal Year: 2023, Volume and Issue: 23, P. 264 - 277
Published: Dec. 5, 2023
Language: Английский
Citations
5
The Crop Journal, Journal Year: 2024, Volume and Issue: 12(4), P. 1064 - 1080
Published: July 30, 2024
Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors. Haploids/doubled haploids (DHs) derived vitro-cultured are widely used plant breeding genetic engineering. However, the mechanism underlying developmental switch regular pollen maturation towards microspore-derived regeneration remains poorly defined. Here, RNA-sequencing was employed to elucidate transcriptional landscapes four early stages microspore embryogenesis (ME) barley cultivars Golden Promise Igri, which exhibit contrasting responsiveness formation. Our experiments revealed fundamental regulatory networks, specific groups genes, transcription factor (TF) families potentially regulating switch. We identified set candidate genes crucial for genotype-dependent responsiveness/recalcitrance ME. high-resolution temporal transcriptome atlas provides an important resource future functional studies on control transition.
Language: Английский
Citations
1
Plant Cell & Environment, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 9, 2024
ABSTRACT Sorghum ( bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development associated agronomic traits remain unexplored. In this study, we performed comprehensive transcriptomic analysis of pistils collected 1–2 days before pollination, developing seeds –2, 10, 20 30 after pollination S. variety M35‐1. Out 31 337 genes expressed in these stages, 12 804 were differentially consecutive stages seed development. These exhibited 10 dominant expression patterns correlated with distinct pathways gene functions. Functional analysis, based on pathway mapping, transcription factor enrichment orthology, delineated key fertilization, early development, filling maturation. Furthermore, colocalization previously reported quantitative trait loci (QTLs) for weight/size revealed 48 mapping to QTL regions. Comprehensive literature mining integrated data shortlisted 25, 17 8 core candidates engineering size, starch protein content, respectively.
Language: Английский
Citations
1
Journal of Agriculture and Food Research, Journal Year: 2024, Volume and Issue: 19, P. 101548 - 101548
Published: Nov. 28, 2024
Language: Английский
Citations
1