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 2020-11-01 to 2024-11-01.)

Article	Citations
Status and prospects of genome‐wide association studies in plants	246
Developing drought‐smart, ready‐to‐grow future crops	107
Introgression of “QTL‐hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars	78
Multitrait machine‐ and deep‐learning models for genomic selection using spectral information in a wheat breeding program	60
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	57
Systems biology for crop improvement	55
The pangenome of banana highlights differences between genera and genomes	38
The application of pangenomics and machine learning in genomic selection in plants	36
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs	35
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program	32
Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping	26
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome	25
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	24
Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene	24
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	22
Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program	22
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes	22
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	22
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize	20
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	20
Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice	20
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	19
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	19
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	18
New insights into homoeologous copy number variations in the hexaploid wheat genome	18

Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	17
Genome‐wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces	17
Genomics‐assisted breeding for successful development of multiple‐stress‐tolerant, climate‐smart rice for southern and southeastern Asia	16
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C₄ enzymes during C₄ evolution in genus Flaveria	16
Deep neural networks for genomic prediction do not estimate marker effects	16
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	16
Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)	16
Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing	16
Identification and fine‐mapping of RppCML496, a major QTL for resistance to Puccinia polysora in maize	16
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	15
Assessing combining abilities, genomic data, and genotype × environment interactions to predict hybrid grain sorghum performance	15
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	15
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	15
Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high‐throughput phenotyping	15
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce	15
A genomics resource for genetics, physiology, and breeding of West African sorghum	15
Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length	15
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	15
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry	14
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	14
Experimental evaluation of genomic selection prediction for rust resistance in sugarcane	14
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	14
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	13
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	13
Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean	13
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	13
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	13
Mineral nutrients in plants under changing environments: A road to future food and nutrition security	13
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	13
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	13
Maize and heat stress: Physiological, genetic, and molecular insights	13
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	13
Integrating genome‐wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus	13
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple	13
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	13
Differential gene expression in tall fescue tissues in response to water deficit	13
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life	13
Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes	12
Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge	12
Deep‐learning power and perspectives for genomic selection	12
Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs	12
Accelerating wheat breeding for end‐use quality through association mapping and multivariate genomic prediction	12
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	12
Diversity, population structure, and linkage disequilibrium among cowpea accessions	12
Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development	12
Genetics of Fusarium head blight resistance in soft red winter wheat using a genome‐wide association study	12
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	11
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	11
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	11
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species	11

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	11
Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment	11
QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice	11
Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL	11
Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola	11
The economics and policy of genome editing in crop improvement	11
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	10
Generalizable approaches for genomic prediction of metabolites in plants	10
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	10
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	10
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	10
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean	10
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	10
Differentially expressed microRNAs that target functional genes in mature soybean nodules	10
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	10
What plant breeding may (and may not) look like in 2050?	10
Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection	10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	10
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	10
De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus	10
Training set design in genomic prediction with multiple biparental families	10
Meta‐QTL s and haplotypes for efficient zinc biofortification of rice	10
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	10
Quantitative and population genomics suggest a broad role of stay‐green loci in the drought adaptation of sorghum	9
Targeted mutagenesis with sequence‐specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects	9
Revealing the contribution of GbPR10.5D1 to resistance against Verticillium dahliae and its regulation for structural defense and immune signaling	9
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	9
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	9
Characterization of heterosis and genomic prediction‐based establishment of heterotic patterns for developing better hybrids in pigeonpea	9
Genetic control of kernel compositional variation in a maize diversity panel	9
“Simple Tidy GeneCoEx”: A gene co‐expression analysis workflow powered by tidyverse and graph‐based clustering in R	9
Understanding role of roots in plant response to drought: Way forward to climate‐resilient crops	9
Genetic dissection of maize plant architecture using a novel nested association mapping population	9
An extensible vector toolkit and parts library for advanced engineering of plant genomes	9
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)	9
Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding	9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	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
Gain from genomic selection for a selection index in two‐row spring barley	8
Genetic diversity for starch quality and alkali spreading value in sorghum	8
Consensus genomic regions for grain quality traits in wheat revealed by Meta‐QTL analysis and in silico transcriptome integration	8
Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441	8
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	8
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize	8
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	8
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	8
Global gene expression analysis of pigeonpea with male sterility conditioned by A₂ cytoplasm	8
Evolution of osmosensing OSCA1 Ca²⁺ channel family coincident with plant transition from water to land	8
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	8
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	8
Single‐nucleotide mosaicism in citrus: Estimations of somatic mutation rates and total number of variants	8
Integrated multi‐omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.)	8
Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed	8
Meta‐analysis of the quantitative trait loci associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits in pigeonpea (Cajanus cajan L.)	8
Characterization of Rsg3, a novel greenbug resistance gene from the Chinese barley landrace PI 565676	8