Plant Genome

(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 2020-02-01 to 2024-02-01.)
Status and prospects of genome‐wide association studies in plants179
Introgression of “QTL‐hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars70
Developing drought‐smart, ready‐to‐grow future crops68
A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction50
Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.)50
Multitrait machine‐ and deep‐learning models for genomic selection using spectral information in a wheat breeding program50
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding48
Systems biology for crop improvement44
A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes43
Genetic control of root anatomical plasticity in maize36
The pangenome of banana highlights differences between genera and genomes33
Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn31
Advancing provitamin A biofortification in sorghum: Genome‐wide association studies of grain carotenoids in global germplasm30
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs30
Genomic selection for lentil breeding: Empirical evidence27
The application of pangenomics and machine learning in genomic selection in plants27
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program26
Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)25
Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress23
Accuracy of genomic selection and long‐term genetic gain for resistance to Verticillium wilt in strawberry22
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome22
Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping22
Genome‐based prediction of multiple wheat quality traits in multiple years20
Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program20
Dominance and G×E interaction effects improve genomic prediction and genetic gain in intermediate wheatgrass (Thinopyrum intermedium)18
Global profiling of N6‐methyladenosine methylation in maize callus induction18
Genetic gains with rapid‐cycle genomic selection for combined drought and waterlogging tolerance in tropical maize (Zea mays L.)18
Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping18
Genome‐wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces17
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat17
Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene17
Identification and fine‐mapping of RppCML496, a major QTL for resistance to Puccinia polysora in maize16
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis16
A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits16
New insights into homoeologous copy number variations in the hexaploid wheat genome15
Making the most of all data: Combining non‐genotyped and genotyped potato individuals with HBLUP15
Pan‐genome: A promising resource for noncoding RNA discovery in plants15
Genomics‐assisted breeding for successful development of multiple‐stress‐tolerant, climate‐smart rice for southern and southeastern Asia14
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs14
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize14
Multiomics approach unravels fertility transition in a pigeonpea line for a two‐line hybrid system14
A genomics resource for genetics, physiology, and breeding of West African sorghum14
Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes14
Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads14
Genome‐wide association analysis of sucrose concentration in soybean (Glycine max L.) seed based on high‐throughput sequencing14
Genome‐based prediction of Bayesian linear and non‐linear regression models for ordinal data14
Genome‐wide association study identifies five new cadmium uptake loci in wheat14
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes14
Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length14
Genomic variation within the maize stiff‐stalk heterotic germplasm pool14
Deep neural networks for genomic prediction do not estimate marker effects13
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C4 enzymes during C4 evolution in genus Flaveria13
Genomic prediction of maternal haploid induction rate in maize13
Accumulation of somatic mutations leads to genetic mosaicism in cannabis13
Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa13
Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing13
Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing13
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce13
Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)13
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing12
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes12
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding12
Integrating genome‐wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus12
Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes12
Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population12
Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat12
Accelerating wheat breeding for end‐use quality through association mapping and multivariate genomic prediction12
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters12
Quantitative trait loci‐based genomics‐assisted prediction for the degree of apple fruit cover color11
Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs11
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials11
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 Caribbean11
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple11
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life11
Genome‐wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.)11
Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL11
Genome‐wide lncRNAs identification and association analysis for cold‐responsive genes at the booting stage in rice (Oryza sativa L.)11
Experimental evaluation of genomic selection prediction for rust resistance in sugarcane10
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 sequencing10
Deep‐learning power and perspectives for genomic selection10
Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat10
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids10
Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean10
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust10
Diversity, population structure, and linkage disequilibrium among cowpea accessions10
Implementing within‐cross genomic prediction to reduce oat breeding costs10
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance10
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association10
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines10
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar9
Assessing combining abilities, genomic data, and genotype × environment interactions to predict hybrid grain sorghum performance9
Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice9
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species9
Four genetic loci control compact plant size with yellow pear‐shaped fruit in ornamental tomato (Solanum lycopersicum L.)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 process9
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks9
Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose9
Quantitative and population genomics suggest a broad role of stay‐green loci in the drought adaptation of sorghum9
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels9
Genetics of Fusarium head blight resistance in soft red winter wheat using a genome‐wide association study9
Differential gene expression in tall fescue tissues in response to water deficit9
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis8
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction8
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis8
QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice8
Responses of cuticular waxes of faba bean to light wavelengths and selection of candidate genes for cuticular wax biosynthesis8
Variance heterogeneity genome‐wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions8
Genome‐wide analysis of PmTCP4 transcription factor binding sites by ChIP‐Seq during pistil abortion in Japanese apricot8
Training set design in genomic prediction with multiple biparental families8
Mapping crown rust resistance at multiple time points in elite oat germplasm8
Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection8
Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection8
Genome‐wide association analysis of natural variation in seed tocochromanols of barley8
Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing8
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study8
Differentially expressed microRNAs that target functional genes in mature soybean nodules8
Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge8
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses8
Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice8