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ARS Home » Research » Manuscripts by Strategic Topical Areas
Plant Genome Mapping
item Haplotype analysis identified key genes associated with improved salt stress tolerance in wheat (Triticum aestivum L.) (Mar 2025)
item Chromosome-level haplotype-resolved genome assembly of bread wheat’s wild relative Aegilops mutica (Mar 2025)
item Understanding iron response mechanisms and carbon partitioning strategies in sorghum under Fe stress (Mar 2025)
item Genomic strategies to improve nitrogen use efficiency and reduce nitrate levels in sorghum forage lines (Mar 2025)
item Characterization of key regulators in microRNA-mediated responses to phosphate deficiency during Arabidopsis root development (Mar 2025)
item Pan-transcriptome of delevoping sorghum meristems reveal putative regulatory targets for mature seed traits (Mar 2025)
item Gramene plants: empowering agricultural research from genomic diversity through pan-genome analysis (Mar 2025)
item Maize data for biology, breeding, and genomics: the pan maize gramene database (Mar 2025)
item Spatial predictions of soil moisture across a longitudinal gradient in semiarid ecosystems using UAVs and RGB sensors (Mar 2025)
item Using Pan-genomes, Databases, and Genomics to Advance Agriculture (Feb 2025)
item Genetic and phenotypic responses of temperature-independent Hessian fly resistant durum wheat to larval attack during heat stress (Feb 2025)
item Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data (Feb 2025)
item Identification of stem rust resistance genes in monogenic lines derived from wheat cultivar Waldron (Feb 2025)
item Quantitative trait loci analysis for anthracnose resistance in a population derived from Andean varieties Bukoba and Kijivu of common bean (Phaseolus vulgaris L.) (Jan 2025)
item Guidelines for gene and genome assembly nomenclature (Jan 2025)
item Breeding strategies to enhance ß-glucan content in oats (Avena sativa L.) (Jan 2025)
item Genomic Prediction and Genome-Wide Association Studies on Biomass Yield under Drought in Alfalfa (Jan 2025)
item Aus sub-population of Oryza sativa L. for bridging food security and water sustainability in rice (Jan 2025)
item Metabolic engineering of lipid biosynthesis enhances oil composition in oat (Jan 2025)
item Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019 (Jan 2025)
item The Construction of Standard Karyotype of Intermediate Wheatgrass and Its Potential Progenitor Species (Jan 2025)
item Empowering Sorghum Research: SorghumBase as a Hub for Genomic Data and Community Collaboration (Jan 2025)
item Deciphering the genetic basis of salt stress tolerance in wheat (Triticum aestivum L.) through association studies and SNP-based haplotype analysis (Jan 2025)
item Insights into the resistance mechanisms of Aegilops umbellulata against leaf rust and bacterial leaf streak using transcriptomics (Jan 2025)
item Registration of three long grain rice germplasm lines with improved blast resistance with the Ptr gene, low chalk, excellent milling quality, and good yield (Jan 2025)
item Genome-wide association studies for seed thermoinhibition in lettuce reveals the interplay of seed age, color, and germination under high temperatures (Jan 2025)
item Genetic and physical localization of Hessian fly resistance genes in barley (Jan 2025)
item Maize and wild relatives show distinct patterns of genome downsizing following polyploidy (Dec 2024)
item Association mapping of drought stress response for yield and quality traits in barley (Dec 2024)
item Development and validation of a quantitative PCR assay method to assess relative resistance of winter wheat to dwarf bunt at early growth stages (Dec 2024)
item Effect of alternate wetting and drying and organic matter addition on greenhouse gas and arsenic dynamics in rice paddy soil (Dec 2024)
item Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) (Dec 2024)
item A barley MLA receptor is targeted by a specialized non-ribosomal peptide effector of the necrotrophic spot blotch fungus to induce disease susceptibility (Dec 2024)
item Dual mechanisms of salinity tolerance in wheat germplasm lines W4909 and W4910 (Nov 2024)
item Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research (Nov 2024)
item Characterization and genomic insights for the emerging rice pathogen, Pantoea ananatis (Nov 2024)
item Lambs grazing with adult ewes prefer forbs with high-nutrient content in native grasslands dominated by Leymus chinensis and Stipa grandis (Nov 2024)
item Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel (Nov 2024)
item Mining the diversity in rice and it’s ancestral species for rice improvement (Nov 2024)
item Genetic mapping of QTLs for resistance to bacterial leaf streak in hexaploid wheat (Nov 2024)
item Genome-wide dissection and haplotype analysis identified superior haplotypes for improved salt stress tolerance in wheat (Triticum aestivum L.) (Nov 2024)
item Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq (Nov 2024)
item A standard area diagram for Fusarium yellows rating in sugar beet (Beta vulgaris L.) (Nov 2024)
item Manifold and spatiotemporal learning on multispectral unoccupied aerial system imagery for phenotype prediction (Nov 2024)
item Prediction of turfgrass quality using multispectral UAV imagery and Ordinal Forests: Validation using a fuzzy approach (Nov 2024)
item Triticum monococcum subsp. monococcum and aegilopoides: new sources of resistance to the dipteran pest, Hessian fly (Diptera: Cecidomyiidae) (Oct 2024)
item Precise, quantitative measurement of sunflower capitulum inclination: a trigonometry-based approach (Oct 2024)
item Fishing for a reelGene: evaluating gene models with evolution and machine learning (Sep 2024)
item Metabolic engineering-induced transcriptome reprogramming enhance oil composition and content in oat (Avena sativa L.) (Sep 2024)
item Identification of two QTL for Hessian fly resistance in tetraploid wheat (Sep 2024)
item Elucidating genetic determinants for salt tolerance in spring wheat (Triticum aestivum L.) (Sep 2024)
item Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement (Sep 2024)
item Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean (Sep 2024)
item Challenges and opportunities of rice disease managements in the USA (Sep 2024)
item Understanding blast resistance through overexpression of the Pita-2 gene in rice (Sep 2024)
item GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement (Sep 2024)
item Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes (Sep 2024)
item Mapping yield related traits in a suite of six oryza rufipogon species complex chromosome segment substitution line libraries in Indica and Japonica rice backgrounds (Sep 2024)
item Improving rice milling quality by identifying and deploying loci affecting kernel fissure resistance (Sep 2024)
item Aus sub-population of Oryza sativa L.: a unique source for improving rice sustainability and climate resiliency related traits in elite US rice varieties (Sep 2024)
item Rice germplasm characterization and enhancement for the sustainability and resilience of the US rice industry using functional genomics toolsand stress tolerance (Sep 2024)
item A scoping review on soil moisture dynamics monitoring in semi-arid ecosystems: methods, techniques and tools applying at different scales (Aug 2024)
item Evaluation of fungicide seed treatmnents for control of chickpea damping-off caused by metalaxyl-resistant Pythium spp. 2023 (Aug 2024)
item Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications (Aug 2024)
item Identification of genetic loci for grain traits and disease resistance reveals a potential trade off in rice (Aug 2024)
item Advances in quantitative genetic analysis in sunflower, applied to breeding programs (Aug 2024)
item The effects of abiotic stressors on rice resistance responses to the blast fungus Magnaporthe oryzae (Aug 2024)
item Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB) (Aug 2024)
item Genomic analysis of sheath blight resistance in rice: identifying resistant accessions and key genetic markers (Aug 2024)
item Functional analysis of a new allele of the broad-spectrum rice blast resistance gene Ptr in weedy species of rice (Aug 2024)
item Protected Rice - Blast resistance genes, genetic markers developed from a cloned major blast resistance gene resulted in more than a dozen U.S. blast resistant rice varieties and germplasm lines (Aug 2024)
item Rice 'Tiara' - High in Antioxidants (Aug 2024)
item Rice 'Jojutla' - Parboiling Quality (Aug 2024)
item Receptor-ligand interactions in the rice blast system revealed by AlphaFold protein structure prediction (Aug 2024)
item Characterization of the uniform regional rice nursery (URRN) for blast and quality using molecular markers for US rice breeding programs. (Aug 2024)
item Development, gene discovery and allele mining of a global tropical japonica core collection (Aug 2024)
item Convergent evolution of plant prickles is driven by repeated gene co-option over deep time (Aug 2024)
item USDA ARS has hidden treasure! genetic discoveries in the USDA collection of world rice varieties (Aug 2024)
item USDA ARS DB NRRC research on rice sustainability and tolerance to biotic & abiotic stresses (Aug 2024)
item USDA ARS develops a new production system for food sustainability and security (Aug 2024)
item USDA ARS develops pre-breeding rice germplasm for enhanced yield, grain quality and stress tolerance (Aug 2024)
item Species-specific microsymbiont discrimination mediated by a Medicago receptor kinase (Jul 2024)
item Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019 (Jul 2024)
item Unraveling the genetic diversity of Magnaporthe oryzae through a graph pangenome approach (Jul 2024)
item From seed shape to genetics: analyzing medicago spp. seed morphology using gwas and machine learning (Jul 2024)
item Identification of blast resistance QTLs in black hull awn weedy rice (RR14) and Aus-196 rice variety (Jul 2024)
item Understanding the impact of seed-borne pantoea ananatis on rice crop (Jul 2024)
item Genomic insights and primer design for the rice pathogen, Pantoea ananatis (Jul 2024)
item Genomic insights for enhanced sheath blight resistance in rice (Oryza sativa L.) (Jul 2024)
item Biological Control of Clubroot of Rapeseed (Plasmodiophora brassicae) by the Endophytic Fungus Didymella macrostoma P2 (Jul 2024)
item Vegetative indices data boost genomic selection models in predicting oat grain yield (Jul 2024)
item Can GWAS information from oat breeding programs be used to develop higher-yield oat varieties? A case study in the SDSU Oat Breeding Program (Jul 2024)
item Complex reticulation in backbone subfamily relationships in Leguminosae (Jul 2024)
item Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability (Jul 2024)
item The identification of the peanut wild relative Arachis stenosperma as a source of resistance to stem rot and analyses of genomic regions conferring disease resistance through QTL mapping (Jul 2024)
item Clover (Trifolium spp.) Inclusion in Kentucky Bluegrass (Poa pratensis) Lawns (Jul 2024)
item Evolution, diversity, and function of the disease susceptibility gene Snn1 in wheat (Jun 2024)
item Association analysis identified candidate genomic regions for heat stress tolerance in bread wheat (Triticum aestivum L.) (Jun 2024)
item Efficacy of red sunflower seed weevil resistance from inbred line cms HA 488 in single-cross hybrids (Jun 2024)
item Receptor- ligand interactions in plant inmate immunity revealed by artificial intelligence AlphaFold (Jun 2024)
item Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model (Jun 2024)
item Genetic mapping of a recessive resistance to stripe rust in barley (Jun 2024)
item Using major resistance genes to manage rice blast disease in the USA (Jun 2024)
item Dissection of nonhost resistance in barley to the heterologous leaf rust pathogen Puccinia triticinay (Jun 2024)
item Discovering bacterial leaf streak disease resistance loci in barley in the interspecific Cytonuclear Multi-Parent Population (CMPP) (Jun 2024)
item Genomic regions associated with spot blotch (SB) resistance in barley in the interspecific cytonuclear multi-parent population (CMPP) (Jun 2024)
item Map-based cloning of the Nec50 gene which regulates programmed cell death in barley (Jun 2024)
item Fine mapping of a QTL conferring susceptibility to spot blotch in barley (Jun 2024)
item SorghumBase: A Public Genetic and Genomic Resource for the Sorghum Community (Jun 2024)
item Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress (May 2024)
item Identifying genomic regions associated with key agro-morphological traits in soft red winter wheat using genome-wide association study (May 2024)
item Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggest negative selection during domestication and breeding (May 2024)
item Future of durum wheat research and breeding: insights from early career researchers (May 2024)
item A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize (May 2024)
item An effector SsCVNH promotes the virulence of Sclerotinia sclerotiorum through targeting class III peroxidase AtPRX71 (May 2024)
item Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii (Apr 2024)
item Current genomic deep learning architectures generalize across grass species but not alleles (Apr 2024)
item Three de novo assembled wild cacao genomes from Upper Amazon reveal new insights into an early divergence of chocolate trees (Apr 2024)
item Genome-wide association study of seed morphology-related traits in sorghum mini core and Senegalese lines (Apr 2024)
item Enhanced pan-genomic resources at the maize genetics and genomics database (Apr 2024)
item Role of moss and Arabidopsis zinc-fnger homeodomain transcription factors in regulating plant architecture (Apr 2024)
item Genome-wide association analysis uncovers genes associated with resistance to head smut pathotype 5 in senegalese sorghum accessions (Mar 2024)
item Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits (Mar 2024)
item Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize (Mar 2024)
item The Hessian fly resistance gene HvRHF1 is localized in an NBS-LRR gene cluster in barley (Mar 2024)
item Elucidating the effect of polyphenol-protein interactions on rheological properties of purple waxy rice (Mar 2024)
item Beet crop wild relative germplasm mining uncovers new sources of disease resistance (Feb 2024)
item MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. (Feb 2024)
item Tetraploid wheat (Triticum turgidum) lines from the United States as a source of Hessian fly (Mayetiola destructor) resistance (Feb 2024)
item Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta) (Feb 2024)
item PanEffect: a pan-genome visualization tool for variant effects in maize (Feb 2024)
item Future outlook of dryland crop production systems in the semi-arid High Plains amid climate change (Feb 2024)
item Hessian fly (Diptera: Cecidomyiidae) virulence in Louisiana: assessment of field populations from 2023 to efficacy of 27 Hessian fly resistance genes in wheat (Jan 2024)
item PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models (Jan 2024)
item Agrobacterium-mediated transfer of the Fusarium graminearum Tri6 gene into barley using mature seed-derived shoot tips as explants (Jan 2024)
item One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa) (Jan 2024)
item Establishing a global Tropical Japonica rice core collection for allele mining and gene discovery: construction, sequencing, and phenotyping (Jan 2024)
item Exploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley (Jan 2024)
item Development of epigenetic landscape and gene expression atlas of oats (Jan 2024)
item Towards improving oil composition and content in oat through metabolic engineering (Jan 2024)
item Genetic mapping of resistance QTLs to bacterial leaf streak in wheat (Jan 2024)
item Identification of QTLs associated with yield components, agronomic traits, and kernel parameters in hard red spring wheat (Jan 2024)
item Telomere-to-telomere genome assembly and resequencing of 20 Aegilops umbellulata genomes reveals broad genetic and phenotypic diversity for novel disease resistance traits (Jan 2024)
item Molecular cloning of the septoria nodorum blotch susceptibility gene Snn2 in wheat (Jan 2024)
item Introduction rice as a model for genetics, genomics, and breeding (Jan 2024)
item Genome-wide association study unravel the genetic basis of seedling heat stress tolerance in wheat (Triticum aestivum L.) (Jan 2024)
item Molecular mapping of a novel genetic locus governing enhanced susceptibility to tan spot in durum wheat (Jan 2024)
item A uniform gene and chromosome nomenclature system for oat (Avena spp.) (Jan 2024)
item Understanding the cocoa genetic resources in the Pacific to assist producers to supply the growing craft market (Dec 2023)
item Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences (Dec 2023)
item Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences (Dec 2023)
item A genomic retrospective of beet breeding progress (Nov 2023)
item Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae) (Nov 2023)
item Introduction of plant transposon annotation for beginners (Nov 2023)
item Untapped sources of dual resistance to Hessian fly and greenbug in synthetic hexaploid wheats (Nov 2023)
item An online database for einkorn wheat to aid in gene discovery and functional genomics studies (Nov 2023)
item Ensembl 2024 (Nov 2023)
item Synergizing Proximal Remote Sensing Modalities for Enhanced Prediction of Key Agronomic Crop Traits (Oct 2023)
item PanEffect: A pan-genome visualization tool for variant effects in maize (Sep 2023)
item Editorial: Advances in Ascochyta Research, Volume II (Sep 2023)
item New whole-genome alignment tools are needed for tapping into plant diversity (Sep 2023)
item Beet crop wild relative germplasm mining uncovers new sources of disease resistance (Sep 2023)
item Transposable element abundance subtly contributes to lower fitness in maize (Sep 2023)
item Quantitative trait locus analysis of Hessian fly resistance in soft red winter wheat (Sep 2023)
item Einkorn genomics sheds light on evolutionary history of the oldest domesticated wheat (Aug 2023)
item Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation (Mar 2023)