OOIR: Observatory of International Research

Papers

(The TQCC of Plant Genome is 7. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-03-01 to 2025-03-01.)

Article	Citations
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	117
Genomic prediction of seed nutritional traits in biparental families of oat (Avena sativa)	62
Integrating de novo QTL‐seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean	61
Genomic prediction for the Germplasm Enhancement of Maize project	60
Identifying and expression analysis of WD40 transcription factors in walnut	41
Research Highlights, The Plant Genome, Volume 15, Issue 4	39
Thanks to Reviewers, The Plant Genome, 2022	37
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	32
Issue Information	28
Combining genome‐wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot	26
DECUSSATEnetwork with flowering genes explains the variable effects ofqDTY12.1to rice yield under drought across genetic backgrounds	24
Shaping the biology of citrus: II. Genomic determinants of domestication	24
Assessment of potential candidate genes for partial resistance to Sclerotinia stem rot caused by Sclerotinia sclerotiorum using real‐time quantitative PCR	24
Maintenance of UK bread baking quality: Trends in wheat quality traits over 50 years of breeding and potential for future application of genomic‐assisted selection	23
The soybean ubiquitin‐proteasome system: Current knowledge and future perspective	23
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Characterization of evolutionarily distinct rice BAHD‐Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani	20
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP	20
Cover Image, Volume 14, Issue 2	20
The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation	20
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	19
Research highlights, The Plant Genome, Volume 16, Issue 3	18
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	18
Evolutionary fates of gene‐body methylation and its divergent association with gene expression in pigeonpea	17
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	16

An extensible vector toolkit and parts library for advanced engineering of plant genomes	16
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	16
Approaches and progress in breeding drought‐tolerant maize hybrids for tropical lowlands in west and central Africa	16
Integrated multi‐omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.)	16
Introducing CHiDO—A No Code Genomic Prediction software implementation for the characterization and integration of driven omics	15
Molecular markers enhance substantially the distinctness of alfalfa varieties for registration and protection	15
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	15
Genetic architecture of protein and oil content in soybean seed and meal	15
Editorial Board	15
Differentially expressed microRNAs that target functional genes in mature soybean nodules	15
Antimicrobial peptides in Dendrobium officinale: Genomic parameters, peptide structures, and gene expression patterns	14
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	14
Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	14
Genomic selection strategies to increase genetic gain in tea breeding programs	14
Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents	14
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	14
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	13
Genetic dissection of domestication traits in interspecific chickpea populations	13
Genomic selection optimization in blueberry: Data‐driven methods for marker and training population design	13
High‐resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust	13
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	13
Genome‐wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments	13
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)	13
Training set design in genomic prediction with multiple biparental families	13
Consensus genomic regions for grain quality traits in wheat revealed by Meta‐QTL analysis and in silico transcriptome integration	13
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	13
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	13
Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean	13
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	12
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	12
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	12
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	12
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	12
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	12
Optimal implementation of genomic selection in clone breeding programs—Exemplified in potato: I. Effect of selection strategy, implementation stage, and selection intensity on short‐term genetic gain	12
Branch angle and leaflet shape are associated with canopy coverage in soybean	12
The trans‐kingdom communication of noncoding RNAs in plant–environment interactions	12
The pangenome of banana highlights differences between genera and genomes	12
Comparing gradient boosting machine and Bayesian threshold BLUP for genome‐based prediction of categorical traits in wheat breeding	11
Development and evaluation of Fusarium wilt‐resistant and high‐yielding chickpea advanced breeding line, KCD 11	11
Genome‐wide association of dry (Tamar) date palm fruit color	11
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	11
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	11
Using cross‐country datasets for association mapping in Arachis hypogaea L.	11
Cover Image, Volume 14, Issue 3	11
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)	11
Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization	11
Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks	11
Use of continuous genotypes for genomic prediction in sugarcane	10

Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	10
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa	10
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	10
Genome‐wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes	10
Combination of meta‐analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean	10
The Plant Genome special section: Grain quality and nutritional genomics for breeding next‐generation crops	10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	10
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	10
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	10
Focusing the GWAS Lens on days to flower using latent variable phenotypes derived from global multienvironment trials	10
Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans	10
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	10
Genetic dissection of seed characteristics in field pennycress via genome‐wide association mapping studies	10
Maize and heat stress: Physiological, genetic, and molecular insights	9
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	9
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	9
The application of pangenomics and machine learning in genomic selection in plants	9
Alfalfa genomic selection for different stress‐prone growing regions	9
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	9
Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China	9
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	9
Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing	9
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	9
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	9
Deep‐learning power and perspectives for genomic selection	9
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	8
Genome‐wide association study of carotenoids in maize kernel	8
Subsampling and DNA pooling can increase gains through genomic selection in switchgrass	8
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks	8
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	8
Recipients of 2021 CSSA Editor's Citation for Excellence Named	8
A medium‐density genotyping platform for cultivated strawberry using DArTag technology	8
Genome‐wide analysis of HD‐Zip genes in Sophora alopecuroides and their role in salt stress response	8
TPG 2021 Publisher's Report	8
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	8
Issue Information	8
Research highlights, The Plant Genome, Volume 16, Issue 2	8
Developing drought‐smart, ready‐to‐grow future crops	8
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	8
Proteomic analysis of near‐isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance	8
Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations	8
Mapping of seed quality traits in the C genome of Brassica napus by using a population carrying genome content of B. oleracea and their effect on other traits	8
Critical roles of the activation of ethylene pathway genes mediated by DNA demethylation in Arabidopsis hyperhydricity	7
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	7
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	7
Genome‐wide association study for yield and quality of granulated cassava processed product	7
Editorial Board	7
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	7
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	7
Simulations of multiple breeding strategy scenarios in common bean for assessing genomic selection accuracy and model updating	7
Thanks to Reviewers, The Plant Genome, 2023	7
Leveraging spatiotemporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models	7
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	7
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing	7
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy	7
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	7
Transcriptome‐wide expression landscape and starch synthesis pathway co‐expression network in sorghum	7
Genome assembly and multi‐omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri	7
Integration of machine learning and genome‐wide association study to explore the genomic prediction accuracy of agronomic trait in oats (Avena sativa L.)	7
Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry	7
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	7
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study	7