Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement DOI Creative Commons
Ahmad H. Sallam, Yu Guo,

Murukarthick Jayakodi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 20, 2024

Abstract To exploit allelic variation in Hordeum vulgare subsp. spontaneum , the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at ∼9X depth, generating 109.5 million single nucleotide polymorphisms after alignment Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait (MTA) on chromosome 1HL close HvBlp cloned gene controlling black lemma. Four MTAs were stem rust resistance: co-locating complex RMRL1-RMRL2 locus 5HL, three novel loci 1HS, 1HL, 5HL. Six days heading (DTH) vernalized plants all chromosomes except 1H 6H. Two DTH non-vernalized 2HS. All novel. The whole genome sequence data described herein will facilitate identification utilization new alleles barley improvement.

Language: Английский

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity DOI Creative Commons
Wenbin Guo, Miriam Schreiber, Vanda Marosi

et al.

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 3, 2025

Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed barley using 20 inbred genotypes representing domesticated by generating analyzing short- long-read RNA-sequencing datasets tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific (RTDs) integrated these into linear pan-genome framework to create pan-RTD, allowing categorization as core, shell or cloud. Focusing on core (expressed all genotypes), observed significant abundance variation among tissues between driven partly RNA processing, gene copy number, structural rearrangements conservation promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations frequent functional diversification. complement pan-transcriptome, comprehensive cultivar (cv.) Morex gene-expression atlas illustrate how combined can be used guide biological inquiry.

Language: Английский

Citations

4
Oxygen sensing and plant adaptation to flooding in a changing climate DOI Creative Commons

Tilo Renziehausen,

A.S. Dirr, Romy Schmidt

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1927)

Published: May 29, 2025

In times of climate change, frequency and intensity extreme weather events are rising thus demand a higher resilience crop plants to environmental influences, such as flooding events, minimize yield losses. Flooding causes acute oxygen deprivation in plants, accompanied by an energy crisis, starvation, growth retardation ultimately increased harvest At molecular level, fluctuating concentrations sensed via plant cysteine oxidases (PCOs) that, part the N-degron pathway, oxygen-dependently oxidize substrates vernalization 2, little zipper 2 and, most prominently, transcription factors group VII ETHYLENE RESPONSE FACTORS (ERFVIIs) render them for degradation. When stabilized under hypoxia owing lack oxygen, ERFVIIs act transcriptional activators hypoxia-response genes evoke appropriate acclimation. Crop engineering improved submergence is important goal future food security, prolonging ERFVII stability promising strategy. Here we discuss potential consequences this strategy terms stabilization Cys-initiating proteins commercially relevant species, well ways which may be achieved, including PCO engineering. This article theme issue ‘Crops stress: can mitigate impacts change on agriculture launch ‘Resilience Revolution’?’.

Language: Английский

Citations

1
Developing pangenomes for large and complex plant genomes and their representation formats DOI Creative Commons

Pradeep Ruperao,

Parimalan Rangan, Trushar Shah

et al.

Journal of Advanced Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct comprehensive landscape, revealing both core and accessory elements. This approach enables identification novel genes, structural variations, gene presence-absence providing insights into species evolution, adaptation, trait variation. Representing requires innovative visualization formats that effectively convey complex structures variations. review delves contemporary methodologies recent advancements in constructing pangenomes, particularly plant genomes. It examines structure pangenome representation, including format comparison, conversion, techniques, their implications for enhancing crop improvement strategies. Earlier comparative have illuminated sequences, copy number variations across diverse concept pan-genome, which captures broad spectrum genotypes, offers holistic perspective species' makeup. However, pan-genome plants with larger genomes poses challenges, managing vast genome sequence comprehending germplasm. To address these researchers explored cost-effective alternatives encapsulate single known as pangenome. involves reducing volume sequences while focusing on With growing prominence genomics, several software tools emerged facilitate construction. sheds light developing utilizing tailored pan-genomes plants. also discusses representation suitable downstream analyses, offering valuable landscape evolutionary dynamics In summary, this underscores significance construction resolving architecture plants, those provides overview advancements, aiding exploring understanding diversity.

Language: Английский

Citations

0
High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity DOI Creative Commons
Zhihui Yuan, Maximilian Rembe, Martin Mascher

et al.

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Background Genebanks around the globe serve as valuable repositories of genetic diversity, offering not only access to a broad spectrum plant material but also critical resources for enhancing crop resilience, advancing scientific research, and supporting global food security. To this end, traditional genebanks are evolving into biodigital resource centers where integration phenotypic genotypic data accessions can drive more informed decision-making, optimize allocation, unlock new opportunities breeding research. However, curation availability interoperable genebank is still in its infancy represents an obstacle rapid discoveries field. Therefore, effectively promoting FAIR (i.e., findable, accessible, interoperable, reusable) these vital maximizing potential driving progress agricultural innovation. Findings Here we provide whole genome sequencing 812 barley (Hordeum vulgare L.) 298 European elite materials released between 1949 2021, well 4 disease resistance traits 3 agronomic traits. The robustness investigated interoperability genomic were assessed current publication, aiming make panel publicly available future research barley. Conclusions showed variability high association mapping potential, key identifying donors with untapped genes advance while safeguarding diversity.

Language: Английский

Citations

0
Genome-wide characterization of two-component system elements in barley enables the identification of grain-specific phosphorelay genes DOI Creative Commons
Christian Hertig,

Pravinya Devunuri,

Twan Rutten

et al.

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 17, 2025

Language: Английский

Citations

0
Plant graph-based pangenomics: techniques, applications, and challenges DOI Creative Commons

Zezhen Du,

Jiabao He, Wen‐Biao Jiao

et al.

aBIOTECH, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Abstract Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating molecular breeding crops. Conventional methods analysis typically rely on small variants, such as SNPs indels, use single linear reference genomes, which introduces biases reduces performance highly divergent regions. By integrating level sequences, pangenomes, particularly graph offer a promising solution to these challenges. To date, numerous algorithms been developed constructing pangenome graphs, aligning reads performing variant genotyping based graphs. As demonstrated various plant pangenomic studies, advancements allow detection previously hidden especially structural thereby enhancing applications mapping agronomically important genes. However, noteworthy challenges remain be overcome applying approaches plants. Addressing issues will require development more sophisticated tailored specifically Such improvements contribute scalability this approach, production super-pangenomes, hundreds or even thousands de novo–assembled genomes from one species genus can integrated. This, turn, promote broader pan-omic further advancing our understanding driving innovations crop breeding.

Language: Английский

Citations

0
INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley DOI Creative Commons

Patrycja Sokolowska,

Matthias Jost, Wolfram Buss

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Abstract DELLA proteins, members of the GRAS-domain family transcriptional regulators, are critical for plant growth and development. They modulate transcription indirectly via interactions with hundreds factors. The phytohormone gibberellin (GA) triggers degradation, providing a mechanism by which plants can integrate developmental environmental signals to regulate gene expression optimize responses. In agriculture, mutations have been instrumental in improving crop performance. Most modern wheat ( Triticum aestivum L.) varieties carry Rht-B1b or Rht-D1b alleles that encode proteins resistant GA-mediated resulting constitutive partial suppression stem growth, semi-dwarf stature lodging resistance. However, these also reduce nitrogen use efficiency early vigour, limiting their utility some environments. Understanding how development is, therefore, refining breeding strategies. this study, we identified orthologous C2H2 zinc-finger factors INDETERMINATE DOMAIN 5 IDD5 ) SEMI-DWARF 3 SDW3 barley Hordeum vulgare as positive regulators leaf expansion. Both physically interact with, act downstream of, key components Altered levels GA biosynthesis genes suggest helps maintain homeostasis addition regulation. Loss-of-function confer GA-insensitive phenotype comparable ‘Green Revolution’ allele, highlighting potential novel dwarfing cereal improvement. Significance statement Our study identifies homologous (IDD5 SDW3) height. Unlike conventional mutations, height but drawbacks such lower nitrogen-use efficiency, IDD may provide more targeted approaches manage growth. By showing promote expansion revealing alternative alleles, our research opens new avenues both fundamental into pathways applications breeding. Ultimately, it could help produce crops improved resistance fewer negative side effects than current alleles.

Language: Английский

Citations

0
Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics DOI Creative Commons

Fu Shi,

Li Li, Mingjie Chen

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(10), P. 1542 - 1542

Published: May 20, 2025

The Oryza genus serves not only as a gene pool for rice improvement but also model system plant evolutionary research. Calcium-dependent protein kinases (CPKs) function both effectors and sensors in calcium signaling play versatile roles development stress responses. Four kinase families, namely CPK-related (CRKs), phosphoenolpyruvate carboxylase (PPCKs), PPCK-related (PEPRKs), calcium- calmodulin-dependent (CCaMKs), are frequently called kinases. This study utilized genomics approaches provided the pan-genome repertoires of CPKs their related 34 genomes by leveraging rich resources Orzya genus. Gene duplication analysis revealed that distinct types contributed to expanding wild rice. We depicted domain architectures kinases, highlighting complexity EF-hand motifs CCaMKs. Transcriptome determined alternative splicing was mechanism contributing diversity generated expression atlas multiple species genus, emphasizing divergent homoeolog patterns across tissues allotetraploid Collectively, our Oryza-wide trajectories highlighted diversified dynamics, providing relatives improvement.

Language: Английский

Citations

0
The 1001G+ project: A curated collection ofArabidopsis thalianalong-read genome assemblies to advance plant research DOI Creative Commons
Carlos Alonso‐Blanco, Haim Ashkenazy, Pierre Baduel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 26, 2024

Abstract Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of reference almost 25 years ago already accompanied by genome-wide data on polymorphisms in another accession, or naturally occurring strain. Since then, inventories diversity have been generated at increasingly precise levels. High-density genotype A. , including those from 1001 Genomes Project, were key to demonstrating enormous power GWAS inbred populations wild plants, and comparison intraspecific polymorphism with interspecific divergence has illuminated many aspects evolution. Over past decade, an increasing number nearly complete sequences published more accessions. Here, we highlight curated collection previously so far unpublished assembled using different types long reads, PacBio Continuous Long Reads (CLR), High Fidelity (HiFi) Oxford Nanopore Technologies (ONT) reads. This Plus (1001G+) resource is being made available http://1001genomes.org . We invite colleagues yet assemblies accessions contribute this effort.

Language: Английский

Citations

1
Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement DOI Creative Commons
Ahmad H. Sallam, Yu Guo,

Murukarthick Jayakodi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 20, 2024

Abstract To exploit allelic variation in Hordeum vulgare subsp. spontaneum , the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at ∼9X depth, generating 109.5 million single nucleotide polymorphisms after alignment Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait (MTA) on chromosome 1HL close HvBlp cloned gene controlling black lemma. Four MTAs were stem rust resistance: co-locating complex RMRL1-RMRL2 locus 5HL, three novel loci 1HS, 1HL, 5HL. Six days heading (DTH) vernalized plants all chromosomes except 1H 6H. Two DTH non-vernalized 2HS. All novel. The whole genome sequence data described herein will facilitate identification utilization new alleles barley improvement.

Language: Английский

Citations

0