OOIR: Observatory of International Research

Papers

(The TQCC of Plant Genome is 8. 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 2020-07-01 to 2024-07-01.)

Article	Citations
Status and prospects of genome‐wide association studies in plants	219
Developing drought‐smart, ready‐to‐grow future crops	90
Introgression of “QTL‐hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars	74
Multitrait machine‐ and deep‐learning models for genomic selection using spectral information in a wheat breeding program	59
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	55
Systems biology for crop improvement	50
A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes	50
The pangenome of banana highlights differences between genera and genomes	37
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs	34
The application of pangenomics and machine learning in genomic selection in plants	33
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program	30
Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping	25
Accuracy of genomic selection and long‐term genetic gain for resistance to Verticillium wilt in strawberry	25
Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress	24
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome	24
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	23
A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits	23
Genome‐based prediction of multiple wheat quality traits in multiple years	21
Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program	21
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	21
Genetic gains with rapid‐cycle genomic selection for combined drought and waterlogging tolerance in tropical maize (Zea mays L.)	21
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	20
Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene	19
Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping	19
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes	19

Pan‐genome: A promising resource for noncoding RNA discovery in plants	18
Genome‐wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces	18
New insights into homoeologous copy number variations in the hexaploid wheat genome	17
Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice	17
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize	17
Genome‐wide association analysis of sucrose concentration in soybean (Glycine max L.) seed based on high‐throughput sequencing	17
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	17
Making the most of all data: Combining non‐genotyped and genotyped potato individuals with HBLUP	17
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	16
Identification and fine‐mapping of RppCML496, a major QTL for resistance to Puccinia polysora in maize	16
Genomics‐assisted breeding for successful development of multiple‐stress‐tolerant, climate‐smart rice for southern and southeastern Asia	16
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	16
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	16
Deep neural networks for genomic prediction do not estimate marker effects	15
Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes	15
A genomics resource for genetics, physiology, and breeding of West African sorghum	15
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce	15
Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length	15
Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)	15
Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa	14
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	14
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C₄ enzymes during C₄ evolution in genus Flaveria	14
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	14
Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing	14
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	14
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry	13
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	13
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	13
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life	13
Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing	13
Assessing combining abilities, genomic data, and genotype × environment interactions to predict hybrid grain sorghum performance	13
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	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
Integrating genome‐wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus	13
Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high‐throughput phenotyping	13
Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes	12
Accelerating wheat breeding for end‐use quality through association mapping and multivariate genomic prediction	12
Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL	12
Quantitative trait loci‐based genomics‐assisted prediction for the degree of apple fruit cover color	12
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	12
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	12
Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean	12
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	12
Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs	12
Experimental evaluation of genomic selection prediction for rust resistance in sugarcane	12
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	12
Deep‐learning power and perspectives for genomic selection	12
Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development	11
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple	11
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	11

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	11
Diversity, population structure, and linkage disequilibrium among cowpea accessions	11
Genetics of Fusarium head blight resistance in soft red winter wheat using a genome‐wide association study	11
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	11
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	11
Responses of cuticular waxes of faba bean to light wavelengths and selection of candidate genes for cuticular wax biosynthesis	11
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	11
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species	10
Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat	10
Construction of high‐density genetic linkage map and mapping quantitative trait loci (QTL) for flowering time in autotetraploid alfalfa (Medicago sativa L.) using genotyping by sequencing	10
Maize and heat stress: Physiological, genetic, and molecular insights	10
Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection	10
Differential gene expression in tall fescue tissues in response to water deficit	10
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	10
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	10
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	10
Evolution of SHORT VEGETATIVE PHASE (SVP) genes in Rosaceae: Implications of lineage‐specific gene duplication events and function diversifications with respect to their roles in process	10
Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola	9
Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge	9
Genome‐wide association analysis of natural variation in seed tocochromanols of barley	9
The economics and policy of genome editing in crop improvement	9
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	9
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	9
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	9
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	9
On Hadamard and Kronecker products in covariance structures for genotype × environment interaction	9
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	9
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	9
Genome‐wide analysis of PmTCP4 transcription factor binding sites by ChIP‐Seq during pistil abortion in Japanese apricot	9
Training set design in genomic prediction with multiple biparental families	9
Quantitative and population genomics suggest a broad role of stay‐green loci in the drought adaptation of sorghum	9
What plant breeding may (and may not) look like in 2050?	9
QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice	9
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	9
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study	9
An extensible vector toolkit and parts library for advanced engineering of plant genomes	9
Targeted mutagenesis with sequence‐specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects	8
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	8
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	8
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	8
De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus	8
Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment	8
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	8
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	8
Generalizable approaches for genomic prediction of metabolites in plants	8
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	8
Differentially expressed microRNAs that target functional genes in mature soybean nodules	8
Evolution of osmosensing OSCA1 Ca²⁺ channel family coincident with plant transition from water to land	8
Characterization of Rsg3, a novel greenbug resistance gene from the Chinese barley landrace PI 565676	8
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize	8
Genome‐wide mapping and prediction of plant architecture in a sorghum nested association mapping population	8
The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth	8
Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing	8
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	8
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	8
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)	8
Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding	8