Updated guidelines for gene nomenclature in wheat

Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(4)

Published: March 23, 2023

Abstract Key message Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the research community. The last decade seen a proliferation genomic resources wheat, including reference- and pan-genome assemblies with gene annotations, which new opportunities to detect, characterise, describe influence traits interest. expansion genetic information supported growth community catalysed strong interest control agronomically important traits, such as yield, pathogen resistance, grain quality, abiotic stress tolerance. To accommodate these developments, present nomenclature wheat. These can be used loci identified based on morphological or phenotypic features name sequence information, similarity characterised other species biochemical properties encoded protein. flexible system is not overly prescriptive but provides structure common framework may extended related cereal species. We propose henceforth facilitate integration data from independent studies allow broader more efficient use text mining approaches, will ultimately help further accelerate breeding.

Language: Английский

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PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1569 - D1578

Published: Oct. 28, 2023

Abstract PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 can help users characterize evolutionary differences similarities among cis-regulatory elements; furthermore, system now in identification of conserved non-coding homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices 18305 factors; expansion helps exploration combinational nucleotide variants elements sequences. Additionally, genomic landscapes factors manually updated, ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) added. Furthermore, statistical review graphical analysis components improved offer intelligible information through analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces regions’ preferences by considering clusters peak visualization all factors, 20 most significantly enriched ontology functions factors. Thus, effectively reconstruct compare across species experiments.

Language: Английский

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Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm

Science, Journal Year: 2025, Volume and Issue: 387(6734), P. 666 - 673

Published: Feb. 6, 2025

Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by tips, leading the patterning of new branches toward available water a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis crop plants. Here, we developed an assay measure maize revealed substantial between tropical/subtropical temperate breeding germplasm that likely resulted divergent selection. Genetic analysis confirmed regulatory role auxin gaseous hormone ethylene locally inhibits branching air-exposed tissues. Our results demonstrate how distinct signaling pathways translate spatial patterns availability developmental programs determine architecture.

Language: Английский

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GrainGenes: a data-rich repository for small grains genetics and genomics

Database, Journal Year: 2022, Volume and Issue: 2022

Published: Jan. 1, 2022

Abstract As one of the US Department Agriculture—Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves data and community needs globally distributed small grains researchers for genetic improvement Triticeae family Avena species that include wheat, barley, rye oat. accomplishes its mission by continually enriching cross-linked content following findable, accessible, interoperable reusable principles, enhancing maintaining an intuitive web interface, creating tools to enable easy access establishing connections within between other biological databases facilitate knowledge discovery. operates database community, collaborates with curators genome sequencing groups contributes AgBioData Consortium International Wheat Initiative through Information System (WheatIS). Interactive linked is paramount successful now has 2917 manually curated gene records, including 289 genes 254 alleles from Gene Catalogue (WGC). There are >4.8 million models in 51 browser assemblies, 6273 quantitative trait loci >1.4 on 4756 physical maps contained 443 mapping sets, complete standardized metadata. Most notably, 50 new browsers outputs Barley PanGenome projects have been created. We provide example expression track Genome Sequencing Chinese Spring wheat demonstrate how tracks can be adapted different types. To help users benefit more data, created four tutorials available YouTube. executing vision service continuously responding global a centralized, long-term, interconnected repository. Database URL:https://wheat.pw.usda.gov

Language: Английский

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Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

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

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m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D194 - D202

Published: Aug. 17, 2023

N 6-Methyladenosine (m6A) is one of the most abundant internal chemical modifications on eukaryote mRNA and involved in numerous essential molecular functions biological processes. To facilitate study this important post-transcriptional modification, we present here m6A-Atlas v2.0, an updated version m6A-Atlas. It was expanded to include a total 797 091 reliable m6A sites from 13 high-resolution technologies two single-cell profiles. Additionally, three methods (exomePeaks2, MACS2 TRESS) were used identify >16 million enrichment peaks 2712 MeRIP-seq experiments covering 651 conditions 42 species. Quality control results samples also provided help users select peaks. We estimated condition-specific quantitative profiles (i.e. differential methylation) under 172 experimental for 19 Further, provide insights into potential functional circuitry, epitranscriptomics annotated with various genomic features, interactions RNA-binding proteins microRNA, potentially linked splicing events single nucleotide polymorphisms. The collected their annotations can be freely queried downloaded via user-friendly graphical interface at: http://rnamd.org/m6a.

Language: Английский

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A leucine‐rich repeat receptor kinase gene confers quantitative susceptibility to maize southern leaf blight

New Phytologist, Journal Year: 2023, Volume and Issue: 238(3), P. 1182 - 1197

Published: Feb. 1, 2023

Summary Southern leaf blight (SLB), caused by the necrotrophic fungal pathogen Cochliobolus heterostrophus (anamorph Bipolaris maydis ), is a major foliar disease which causes significant yield losses in maize worldwide. A quantitative trait locus, qSLB 3.04 , conferring recessive resistance to SLB was previously mapped on chromosome 3. Using combination of map‐based cloning, association analysis, ethyl methanesulfonate and transposon mutagenesis, CRISPR‐Cas9 editing, we demonstrate that leucine‐rich repeat receptor‐like kinase gene have called ChSK1 ( Susceptibility Kinase 1 ) at increased susceptibility SLB. Genes this type generally been associated with defense response. We present evidence may be suppression basal immune These findings contribute our understanding plant genes potential use them for engineering durable resistance.

Language: Английский

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Exploring impact of recombination landscapes on breeding outcomes

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(14)

Published: March 27, 2023

Plant breeding relies on crossing-over to create novel combinations of alleles needed confer increased productivity and other desired traits in new varieties. However, crossover (CO) events are rare, as usually only one or two them occur per chromosome each generation. In addition, COs not distributed evenly along chromosomes. plants with large genomes, which includes most crops, predominantly formed close ends, there few the swaths around centromeres. This situation has created interest engineering CO landscape improve efficiency. Methods have been developed boost globally by altering expression anti-recombination genes increase rates certain parts changing DNA methylation patterns. progress is being made devise methods target specific sites. We review these approaches examine using simulations whether they indeed capacity efficiency programs. found that current alter can produce enough benefits for programs be attractive. They genetic gain recurrent selection significantly decrease linkage drag donor loci schemes introgress a trait from unimproved germplasm an elite line. genome sites were also provide advantage when introgressing segment harboring desirable quantitative loci. recommend avenues future research facilitate implementation

Language: Английский

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The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(15), P. 4611 - 4624

Published: June 14, 2024

Abstract Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret ever-increasing number of reported PTMs, Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview PTMs tools to assess it. This update includes 62 novel profiling studies, adding a total 112 000 modified peptides reporting including 14 additional types three species (moss, tomato, soybean). Furthermore, open modification re-analysis large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes lysine acylations predominant in seed flower tissues 3-phosphoglycerylation on glycolytic enzymes plants. An extra ‘Protein list analysis’ tool was developed for retrieval assessing enrichment interest. We conducted analysis nuclear proteins, revealing substantial redox nucleus, confirming previous assumptions regarding regulation transcription. encourage use 2.0 hypothesis testing new target discovery, also submit data expand coverage conditions, species, types, thereby enriching our understanding biology.

Language: Английский

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Structural Variants Contribute to Phenotypic Variation in Maize

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

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