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Chloroplasts fuel plant development and growth by converting solar energy into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley (Hordeum vulgare) has greatly broadened the field of chloroplast biology, including the discovery of retrograde signaling. Here, we report identification of the ALBOSTRIANS gene HvAST (also known as Hordeum vulgare CCT Motif Family gene 7, HvCMF7) by positional cloning as well as its functional validation based on independently induced mutants by Targeting Induced Local Lesions in Genomes (TILLING) and RNA-guided clustered regularly interspaced short palindromic repeats-associated protein 9 endonuclease-mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvCMF7 in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvCMF7 is a homolog of the Arabidopsis (Arabidopsis thaliana) CONSTANS, CO-like, and TOC1 (CCT) Motif transcription factor gene CHLOROPLAST IMPORT APPARATUS2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Notably, in barley we localized HvCMF7 to the chloroplast, without any clear evidence for nuclear localization.

Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that provides cost-effective access to the diversity present in the whole set. Software like Core Hunter 3 is available to generate high quality core sets. In addition, general clustering approaches, e.g. , k -medoids, are available to subdivide a large data set into small groups with maximum genetic diversity between groups.Illumina genotyping platforms are a very efficient tool for the assessment of genetic diversity of plant genetic resources. The accumulation of genotyping data over time using commercial genotyping platforms raises the question of how such huge amount of information can be efficiently used for creating core collections. In the present study, after developing a 15K wheat Infinium array with 12,908 SNPs and genotyping a set of 479 hexaploid winter wheat lines ( Triticum aestivum ), a larger data set was created by merging 411 lines previously genotyped with the 90K iSelect array. Overlaying the markers from the 15K and 90K arrays enabled the identification of a common set of 12,806 markers, suggesting that the 15K array is a valuable and cost-effective resource for plant breeding programs.Finally, we selected genetically diverse core sets out of these 890 wheat genotypes derived from five collections based on the common markers from the 15K and 90K SNP arrays. Two different approaches, k -medoids and Core Hunter 3 were compared,and k -medoids was identified as an efficient method for selecting small core sets out of a large collection of genotypes while retaining the genetic diversity of the original population.

Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the acreage. These requirements for improved plant cultivars can be supported by the broader exploitation of plant genetic resources (PGR) as inputs for genomics-assisted breeding. To support this process we have developed BRIDGE, a data warehouse and exploratory data analysis tool for genebank genomics of barley ( L.). Using efficient technologies for data storage, data transfer and web development, we facilitate access to digital genebank resources of barley by prioritizing the interactive and visual analysis of integrated genotypic and phenotypic data. The underlying data resulted from a barley genebank genomics study cataloging sequence and morphological data of 22,626 barley accessions, mainly from the German Federal genebank. BRIDGE consists of interactively coupled modules to visualize integrated, curated and quality checked data, such as variation data, results of dimensionality reduction and genome wide association studies (GWAS), phenotyping results, passport data as well as the geographic distribution of germplasm samples. The core component is a manager for custom collections of germplasm. A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic data in MIAPPE-compliant ISA-Tab files. BRIDGE is accessible at the following URL: https://bridge.ipk-gatersleben.de.

Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement.We analyzed the recessivemutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected

Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a pre-breeding program.

Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.

Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community.

Cassava is a vital staple crop, yet genomic resources for diverse ecotypes, particularly from key regions, remain limited. To address this, we generated high-quality genome assemblies for nine Thai M. esculenta cultivars and one wild relative, Manihot glaziovii . The sequencing strategy combined Oxford Nanopore long reads for initial assembly with Illumina short reads for polishing and quality assessment. For five of the genotypes, extensive RNA-Seq data from various tissues and developmental stages were also produced to guide gene annotation. We provide detailed technical validation of the ten genome assemblies, reporting on key metrics of contiguity (N50s from 28.9 to 35.2 Mb), completeness (Complete BUSCO scores from 95.69% to 99.21%), and base-level accuracy ( k -mer QV scores from 33.47 to 37.67). The final annotated assemblies and all raw sequencing data have been deposited in public archives and are readily accessible. These datasets represent a significant expansion of the genomic toolkit for Asian cassava, providing a foundational resource for future genetic discovery, comparative genomics, and advanced breeding applications.

Plant pan-genomes, which aggregate genomic sequences and annotations from multiple individuals of a species, have emerged as transformative tools for understanding genetic diversity, adaptation, and evolutionary dynamics. Super-pan-genomes, extending across species boundaries, further enable comparative analyses of clades or genera, bridging breeding applications with evolutionary insights (Shang et al., 2022; Li et al., 2023a). However, the absence of standardized practices for data generation, analysis, and sharing hinders reproducibility and interoperability. This white paper presents a harmonized framework developed by the ELIXIR E-PAN consortium, addressing nomenclature, quality control (QC), data formats, visualization, and community practices. By adopting these guidelines, researchers can enhance FAIR (Findable, Accessible, Interoperable, Reusable) compliance, foster collaboration, and accelerate translational applications in crop improvement and evolutionary biology.