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 2020-05-01 to 2024-05-01.)

Article	Citations
Status and prospects of genome‐wide association studies in plants	202
Developing drought‐smart, ready‐to‐grow future crops	80
Introgression of “QTL‐hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars	72
Multitrait machine‐ and deep‐learning models for genomic selection using spectral information in a wheat breeding program	55
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	50
Systems biology for crop improvement	47
A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes	46
The pangenome of banana highlights differences between genera and genomes	35
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs	32
The application of pangenomics and machine learning in genomic selection in plants	30
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program	27
Accuracy of genomic selection and long‐term genetic gain for resistance to Verticillium wilt in strawberry	25
Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping	24
Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress	23
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome	22
Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program	21
A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits	20
Genetic gains with rapid‐cycle genomic selection for combined drought and waterlogging tolerance in tropical maize (Zea mays L.)	20
Genome‐based prediction of multiple wheat quality traits in multiple years	20
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	19
Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping	19
Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene	18
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	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
Making the most of all data: Combining non‐genotyped and genotyped potato individuals with HBLUP	17

New insights into homoeologous copy number variations in the hexaploid wheat genome	16
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	16
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes	16
Pan‐genome: A promising resource for noncoding RNA discovery in plants	16
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	16
Identification and fine‐mapping of RppCML496, a major QTL for resistance to Puccinia polysora in maize	16
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize	15
Genome‐based prediction of Bayesian linear and non‐linear regression models for ordinal data	15
A genomics resource for genetics, physiology, and breeding of West African sorghum	15
Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes	15
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	15
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	15
Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length	15
Genome‐wide association analysis of sucrose concentration in soybean (Glycine max L.) seed based on high‐throughput sequencing	15
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	15
Genomics‐assisted breeding for successful development of multiple‐stress‐tolerant, climate‐smart rice for southern and southeastern Asia	15
Genome‐wide association study identifies five new cadmium uptake loci in wheat	14
Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)	14
Deep neural networks for genomic prediction do not estimate marker effects	14
Multiomics approach unravels fertility transition in a pigeonpea line for a two‐line hybrid system	14
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	14
Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing	13
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	13
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C₄ enzymes during C₄ evolution in genus Flaveria	13
Genome‐wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.)	13
Integrating genome‐wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus	13
Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice	13
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce	13
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	13
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	13
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	13
Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing	13
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	13
Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes	12
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	12
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life	12
Experimental evaluation of genomic selection prediction for rust resistance in sugarcane	12
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	12
Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population	12
Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat	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
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	12
Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs	11
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple	11
Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	11
Assessing combining abilities, genomic data, and genotype × environment interactions to predict hybrid grain sorghum performance	11
Genome‐wide lncRNAs identification and association analysis for cold‐responsive genes at the booting stage in rice (Oryza sativa L.)	11
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	11
Quantitative trait loci‐based genomics‐assisted prediction for the degree of apple fruit cover color	11

Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	10
Responses of cuticular waxes of faba bean to light wavelengths and selection of candidate genes for cuticular wax biosynthesis	10
Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean	10
Deep‐learning power and perspectives for genomic selection	10
Diversity, population structure, and linkage disequilibrium among cowpea accessions	10
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	10
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry	10
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	10
Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat	10
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	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
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species	10
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	10
Quantitative and population genomics suggest a broad role of stay‐green loci in the drought adaptation of sorghum	9
The economics and policy of genome editing in crop improvement	9
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	9
An extensible vector toolkit and parts library for advanced engineering of plant genomes	9
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	9
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	9
Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection	9
Genetics of Fusarium head blight resistance in soft red winter wheat using a genome‐wide association study	9
Differential gene expression in tall fescue tissues in response to water deficit	9
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	9
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	9
QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice	9
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	9
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study	9
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	9
Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development	9
Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola	8
Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge	8
Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high‐throughput phenotyping	8
Generalizable approaches for genomic prediction of metabolites in plants	8
Maize and heat stress: Physiological, genetic, and molecular insights	8
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	8
Differentially expressed microRNAs that target functional genes in mature soybean nodules	8
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	8
On Hadamard and Kronecker products in covariance structures for genotype × environment interaction	8
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	8
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	8
Genome‐wide analysis of PmTCP4 transcription factor binding sites by ChIP‐Seq during pistil abortion in Japanese apricot	8
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	8
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	8
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	8
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	8
Genome‐wide association analysis of natural variation in seed tocochromanols of barley	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
Training set design in genomic prediction with multiple biparental families	8