Two papers in this issue focused ... accuracy of genomic prediction for several agronomic traits, including grain yield, plant height, and spike length [6]. In addition, the paper on salt tolerance improvement in rice shows how SNP marker-assisted selection can be combined with ...

GS can be enhanced by phenomics, metabolomics, transcriptomics, and enviromics data to improve prediction accuracy. Deep learning (DL)-based GS is expected to facilitate the integration of multiple layers of information in prediction models. Emerging technologies, research, and agricultural challenges continuously shape the role of GS in plant breeding. ... GWAS dissect complex traits by testing genome-wide SNPs across an assembled population.

Plant Systems Biology. Rebecca Dewhirst, a postdoc at LBNL, studies leaf water potential of poplar trees in response to an experimental drought. [Courtesy LBNL]The Genomic Science Program (GSP) recognizes that gene function determination has not kept pace with omics data acquisition and that this incongruence represents an ascending challenge for the research community.

In particular, we look at the extent ... evolution of gene families. ... Plant genomes span several orders of magnitude in size, vary in levels of ploidy and heterozygosity, and contain old and recent bursts of transposable elements, which render them challenging but interesting ...

January 4, 2024 - The Plant GDB Genome Browser displays current gene structure models and transcript evidence from spliced alignments of EST and cDNA sequences. If applicable, matched GSS contigs, community annotations, similar proteins, and microarray probes ...

Check which features are supported on each species here; if you would like to request a new species please email Helpdesk. The new Ensembl provides access to over 4700 genomes: http://beta.ensembl.org · There are over 4100 animal, 470 plant, and 100 fungal genomes ready to explore.

Here, the authors report the genome assemblies of three Curcuma species and find that terpene synthase genes quite often become pseudogenes inside an inversion, indicating inversions act as a counteracting force against gene tandem duplication. ... A chromosome-level genome assembly for Angelica sinensis var. Qinggui1 combined with metabolomic and transcriptomic analyses provides insight into the pathways involved in the biosynthesis of pharmaceutically important compounds in roots of this plant.

Explore the complexity of plant genomes! Discover insights on polyploidy, genome duplication, and advanced sequencing for sustainable agriculture.

Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced.

Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms. Key terms: genomics, Arabidopsis thaliana, Oryza sativa, plant breeding, gene discovery ... Until very recently, the molecular analysis of plants often focused on the single gene level.

October 19, 2020 - The plant DNA C-values database (release 7.1): An updated online repository of plant genome size data for comparative studies. New Phytologist, 226, 301–305. https://doi.org/10.1111/nph.16261 ... Pteridophyte Phylogeny Group (PPG) (2016). A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution, 54, 563–603. ... Puttick, M. N., Clark, J. W., & Donoghue, P. C. J. (2015). Size is not everything: Rates of genome size evolution, not C-value, correlate with speciation in angiosperms.

January 15, 2026 - CNRGV is a repository center for all these plant genomic libraries and also a service provider dedicated to the scientific community.

Identifying the causal mutation of a phenotype can be accelerated by combining genetic mapping with whole genome sequencing, in a process termed mapping-by-sequencing, and James et al. [9] describe important new guidelines for mapping-by-sequencing in Arabidopsis. They generate a Perl-based simulation tool called Pop-seq, which simulates mapping populations to determine the number of plants and the sequencing depth required to identify candidate mutations in outcrossed and backcrossed mapping populations.

[8] summarizes recent developments in plant genomics and their application, with an emphasis on cereal crops. They discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, gene editing using CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. Noncoding RNAs (ncRNAs) modulate mRNA or protein profiles. ncRNAs are essential for growth and development in plants and have emerged as key players in guarding plants during stress conditions.

December 29, 2025 - Genes involved in stress tolerance, such as those controlling water-use efficiency or salinity tolerance, can be identified through genomic studies. Research demonstrates that drought tolerance is a complex quantitative trait regulated by multiple genes, representing one of the most challenging characteristics to study and classify in plant breeding. The PlantArray system enables researchers to test these genetic findings by simulating stress conditions and monitoring plant responses.

January 14, 2026 - Mitochondrial DNA encodes around 13 proteins and is heavily reliant on information from the nucleus and their own genome for proper functioning. Extensive studying of mitochondrial DNA is very important for evolutionary research, migration patterns and insight into genetic disease. Chloroplast DNA (cpDNA): This is genetic information found within the chloroplasts of plant cells.

3 weeks ago - It mainly provides genome sequences, gene models, functional annotations and polymorphic loci. For some of the plant species, additional information is provided including population structure, individual genotypes, linkage, and phenotype data. Gramene is an online web database resource for ...

Reviews of the Human Genome Project, the Drosophila Genome Project, and the Arabidopsis Genome Sequencing Project provided insights on how to identify and prioritize the logical next steps needed to understand the genomics of plants. Many of the molecular genetic and bioinformatic tools in those programs can either be directly adopted or point the way toward needs specific for plants.

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes ...

November 29, 2021 - The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand ...