Plant Molecular Biology, Journal Year: 2022, Volume and Issue: 111(1-2), P. 73 - 88
Published: Nov. 14, 2022
Language: Английский
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: Sept. 22, 2023
The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice gene GSE9 contributes to grain shape difference indica/xian and japonica/geng varieties. evolves previous region wild Oryza rufipogon through the acquisition start codon. This is inherited by most japonica varieties, while original sequence (absence codon, gse9) present majority indica Knockout varieties leads slender grains, whereas introgression background results round grains. Population evolutionary analyses reveal gse9 are derived Or-I Or-III groups, respectively. Our findings uncover genetic divergence subspecies, provide target for precise manipulation shape.
Language: Английский
Citations
26
PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(3), P. 2111 - 2128
Published: Feb. 15, 2024
Abstract For successful double fertilization in flowering plants (angiosperms), pollen tubes deliver 2 nonmotile sperm cells toward female gametes (egg and central cell, respectively). Heatwaves, especially during the reproduction period, threaten male gametophyte (pollen) development, resulting severe yield losses. Using maize (Zea mays) as a crop grass model system, we found strong seed set reduction when moderate heat stress was applied for d uni- bicellular stages of development. We show that accelerates development impairs germination capabilities at unicellular stage. Heat stage cell transport into tubes. To understand course latter defects, used marker lines analyzed transcriptomes isolated cells. affected expression genes associated with transcription, RNA processing translation, DNA replication, cycle. This included encoding centromeric histone 3 (CENH3) α-tubulin. Most were misregulated encode proteins involved transition from metaphase to anaphase mitosis II. also activated spindle assembly check point meta- In summary, misregulation identified results defects ultimately leading sterility.
Language: Английский
Citations
15
Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 13, 2025
ABSTRACT Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic but we lack methods that can detect polymorphic SVs and TEs using short‐read sequencing data. Here, used a whole genome alignment between two maize genotypes identify then genotyped large diversity panel for these After characterising SV panel, identified polymorphisms associated with life history traits genotype‐by‐environment (GxE) interactions. While most contained TEs, only had boundaries clearly matched TE breakpoints indicative insertion, while other were caused by deletions. One appeared be insertion associations gene expression compared trait‐associated SVs. All linkage disequilibrium nearby single nucleotide (SNPs), suggesting approach here did not unique would have missed SNP association study. Overall, (1) created technique genotype across support from genomic alignments (2) connected this presence/absence diverse GxE
Language: Английский
Citations
1
Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D107 - D114
Published: Nov. 22, 2023
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene protein expression localisation in bulk at single cell level. These resources aim to allow users investigate their normal tissue (baseline) or response perturbations such as disease changes genotype (differential) across multiple species. Users invited search genes metadata terms species biological conditions a standardised consistent interface. Alongside these data, new features query through our type wheel search. At experiment level data can be explored two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) Uniform Manifold Approximation Projection (UMAP), overlaid with either clustering information assist users' understanding. Data also visualised marker heatmaps identifying that help confer cluster identity. For some additional visualisations available interactive anatomograms heatmaps.
Language: Английский
Citations
15
Database, Journal Year: 2023, Volume and Issue: 2023
Published: Jan. 1, 2023
Abstract Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function evolution facilitate genomic selection. These datasets hold immense value for both current future studies, as they are vital crop breeding, yield improvement overall agricultural sustainability. However, integrating these from heterogeneous sources presents significant challenges hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 a part of AgBioData Consortium (https://www.agbiodata.org) review types resources that support archiving, analysis visualization needs plant research community. For 2021–22, we identified different examined metadata annotations related experimental design/methods/sample collection, etc. Furthermore, thoroughly reviewed publicly funded repositories raw processed well secondary databases knowledgebases enable integration context genome browser, pathway networks tissue-specific expression. Based on our survey, recommend need (i) additional infrastructural archiving many new types, (ii) development community standards annotation formatting, (iii) biocuration (iv) tools connect with enhance knowledge synthesis foster translational research. Although this paper only covers relevant community, expect similar issues shared by researchers working animals. Database URL: https://www.agbiodata.org.
Language: Английский
Citations
14
PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(1), P. 67 - 76
Published: May 29, 2024
Abstract Noncanonical peptides (NCPs) are a class of generated from regions previously thought as noncoding, such introns, 5′ UTRs, 3′ and intergenic regions. In recent years, the significance diverse functions NCPs have come to light, yet systematic comprehensive NCP database remains absent. Here, we developed NCPbook (https://ncp.wiki/ncpbook/), evidence-supported NCPs, which aims provide resource for efficient exploration, analysis, manipulation NCPs. incorporates data public databases scientific literature. The current version includes 180,676 across 29 different species, evidenced by MS, ribosome profiling, or molecular experiments. These distributed kingdoms, comprising 123,408 14 plant 56,999 7 animal 269 8 microbial species. Furthermore, encompasses 9,166 functionally characterized playing important roles in immunity, stress resistance, growth, development. Equipped with user-friendly interface, allows users search, browse, visualize, retrieve data, making it an indispensable platform researching various plant, animal,
Language: Английский
Citations
5
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: March 8, 2023
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable milling thereby lowering head rice recovery its market price. Availability of multiple QTLs associated with chalkiness attributes, provided us opportunity perform a meta-analysis identify candidate genes their alleles contributing enhanced quality. From 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant were identified. MQTL analysis reduced genetic physical intervals nearly 73% meta-QTLs narrower than 5cM 2Mb, revealing hotspot genomic regions. By investigating expression profiles published datasets, 49 shortlisted on basis differential regulation at least two datasets. We identified non-synonymous allelic variations haplotypes 39 across 3K genome panel. Further, we phenotyped subset panel 60 accessions by exposing them temperature stress under natural field conditions over Rabi cropping seasons. Haplo-pheno uncovered haplotype combinations synthesis genes, GBSSI SSIIa, significantly towards formation chalk rice. We, therefore, report not only markers pre-breeding material, but also propose superior which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing generate elite varieties HRY traits.
Language: Английский
Citations
12
Genes, Journal Year: 2023, Volume and Issue: 14(9), P. 1673 - 1673
Published: Aug. 24, 2023
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many resistance genes receptor-like kinases (RLKs) are recruited early on host plant to respond pathogens. Wall-associated receptor (WAKs), a subfamily kinases, have been shown play role fungal defense. The gene WAK91 (OsWAK91), co-located major SB QTL region chromosome 9, was identified us as candidate defense against blight. An SNP mutation T/C susceptible variety Cocodrie (CCDR) resistant line MCR010277 (MCR). consequence allele C is stop codon loss, resulting an open reading frame with extra 62 amino acid carrying longer protein kinase domain additional phosphorylation sites. Our genotype phenotype analysis parents CCDR MCR top 20 individuals double haploid population strongly correlate SNP. T present japonica subspecies most tropical temperate lines. Multiple US commercial varieties background carry known for susceptibility. This discovery opens possibility introducing alleles into high-yielding reduce losses incurred disease.
Language: Английский
Citations
12
Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(23)
Published: May 28, 2024
Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing high‐throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately haplo-genomes both revealed structural variations between haplotypes a given cultivar. deletions/insertions, inversions, translocations, duplications provide insight into evolutionary history parental relationship among grape varieties. Integration de novo single full-length transcript isoforms (Iso-Seq) yielded highly improved annotation. Given its higher contiguity, robustness IsoSeq-based annotation, assembly meets standard become annotated reference V. . Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides browser integrated web tools expression profiling, set statistical (StatTools) identification correlated genes. Implementation correlation finder tool MybA1 , major regulator anthocyanin pathway, identified candidate genes associated with metabolism, whose patterns experimentally validated as discriminating black white grapes. These resources innovative mining genome-related data are anticipated foster advances in several areas grapevine research.
Language: Английский
Citations
4
The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)
Published: April 1, 2025
The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding breeding improvement. While there are several single-species-specific plant databases, availability multi-species databases is limited. Additionally, variations in methods data types used analysis across different hinder comparison integration information from various projects at or single-species levels. To tackle this challenge, we introduce PlantPan, comprehensive database housing results 195 genomes 11 species. PlantPan aims to provide extensive information, including gene-centric sequence-centric graph-based pan-genome, openness profiles, gene functions its variation characteristics, homologous genes, clusters Statistically, incorporates 9 163 011 694 191 clusters, 526 973 370 genome variations, 1 616 089 non-redundant groups level, 33 455,098 synteny, 177 827 synteny level. Regarding functional contains 5 222 720 genes related transcription factors, 395 247 literature-reported resistance 455 748 predicted microbial/disease 612 112 molecular pathways. In summary, vital platform advancing application pan-genomes crops evolutionary research plants.
Language: Английский
Citations
0