Plant Genome

Article	Citations
Status and prospects of genome‐wide association studies in plants	195
Developing drought‐smart, ready‐to‐grow future crops	77
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	54
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	49
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	24
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
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
A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits	20
Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping	19
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	19
Global profiling of N6‐methyladenosine methylation in maize callus induction	18
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
Making the most of all data: Combining non‐genotyped and genotyped potato individuals with HBLUP	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
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‐enabled prediction for sparse testing in multi‐environmental wheat trials	15
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	15
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	15
New insights into homoeologous copy number variations in the hexaploid wheat genome	15
Genome‐wide association analysis of sucrose concentration in soybean (Glycine max L.) seed based on high‐throughput sequencing	15
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	15
Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes	15
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes	15
Pan‐genome: A promising resource for noncoding RNA discovery in plants	15
Genomics‐assisted breeding for successful development of multiple‐stress‐tolerant, climate‐smart rice for southern and southeastern Asia	15
Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length	15
A genomics resource for genetics, physiology, and breeding of West African sorghum	14
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	14
Deep neural networks for genomic prediction do not estimate marker effects	14
Genome‐based prediction of Bayesian linear and non‐linear regression models for ordinal data	14
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
Multiomics approach unravels fertility transition in a pigeonpea line for a two‐line hybrid system	14
Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing	13
Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice	13
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C4 enzymes during C4 evolution in genus Flaveria	13
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	13
Integrating genome‐wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus	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
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	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
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce	13
Genome‐wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.)	13
Accelerating wheat breeding for end‐use quality through association mapping and multivariate genomic prediction	12
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life	12
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	12
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	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
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
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
Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes	12
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple	11
Quantitative trait loci‐based genomics‐assisted prediction for the degree of apple fruit cover color	11
Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs	11
Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL	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
Diversity, population structure, and linkage disequilibrium among cowpea accessions	10
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	10

Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean	10
Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	10
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	10
Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat	10
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	10
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species	10
Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	10
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	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
Deep‐learning power and perspectives for genomic selection	10
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	10
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	9
Four genetic loci control compact plant size with yellow pear‐shaped fruit in ornamental tomato (Solanum lycopersicum L.)	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
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	9
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	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
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	9
Quantitative and population genomics suggest a broad role of stay‐green loci in the drought adaptation of sorghum	9
QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice	9
Responses of cuticular waxes of faba bean to light wavelengths and selection of candidate genes for cuticular wax biosynthesis	8
The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth	8
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study	8
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	8
Training set design in genomic prediction with multiple biparental families	8
Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola	8
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	8
Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection	8
Genome‐wide association analysis of natural variation in seed tocochromanols of barley	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
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	8
Differentially expressed microRNAs that target functional genes in mature soybean nodules	8
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	8
Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high‐throughput phenotyping	8
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	8
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry	8
Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing	8
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	8
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	8
An extensible vector toolkit and parts library for advanced engineering of plant genomes	8
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	8
Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development	8
Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge	8
De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus	7
On Hadamard and Kronecker products in covariance structures for genotype × environment interaction	7
Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding	7
Gain from genomic selection for a selection index in two‐row spring barley	7
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	7
Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment	7
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize	7
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	7
A multigenotype maize silk expression atlas reveals how exposure‐related stresses are mitigated following emergence from husk leaves	7
The economics and policy of genome editing in crop improvement	7
Non‐homology‐based prediction of gene functions in maize (Zea mays ssp. mays)	7
Global gene expression analysis of pigeonpea with male sterility conditioned by A2 cytoplasm	7
Characterization of Rsg3, a novel greenbug resistance gene from the Chinese barley landrace PI 565676	7
Genetic control of kernel compositional variation in a maize diversity panel	7
Genome‐wide mapping and prediction of plant architecture in a sorghum nested association mapping population	7
Generalizable approaches for genomic prediction of metabolites in plants	7
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	6
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	6
Identification and assessment of alleles in the promoter of the Cyc‐B gene that modulate levels of β‐carotene in ripe tomato fruit	6
Characterization of heterosis and genomic prediction‐based establishment of heterotic patterns for developing better hybrids in pigeonpea	6
New tools for characterizing early brown stem rot disease resistance signaling in soybean	6
Single‐nucleotide mosaicism in citrus: Estimations of somatic mutation rates and total number of variants	6
Maize and heat stress: Physiological, genetic, and molecular insights	6
Genome‐wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments	6
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	6
Genetic diversity for starch quality and alkali spreading value in sorghum	6
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	6
Identifying and expression analysis of WD40 transcription factors in walnut	6
Integrated multi‐omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.)	6
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)	6
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	6
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	6
Predicting metabolic pathways of plant enzymes without using sequence similarity: Models from machine learning	5
Genome‐wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel	5
A novel adult plant leaf rust resistance gene Lr2K38 mapped on wheat chromosome 1AL	5

Targeted mutagenesis with sequence‐specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects	5
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations	5
Integration of metabolomics and transcriptomics data to further characterize Gliricidia sepium (Jacq.) Kunth under high salinity stress	5
Genetic dissection of maize plant architecture using a novel nested association mapping population	5
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	5
Selection signatures across seven decades of hard winter wheat breeding in the Great Plains of the United States	5
Haploidy and aneuploidy in switchgrass mediated by misexpression of CENH3	5
Meta‐analysis of the quantitative trait loci associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits in pigeonpea (Cajanus cajan L.)	5
“Simple Tidy GeneCoEx”: A gene co‐expression analysis workflow powered by tidyverse and graph‐based clustering in R	5
Environment characterization and genomic prediction for end‐use quality traits in soft white winter wheat	5
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	5
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	5
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	5
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	5
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	5
Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents	5
Genetic and QTL mapping in African bermudagrass	5
Genetic control of grain amino acid composition in a UK soft wheat mapping population	5
Evolution of osmosensing OSCA1 Ca2+ channel family coincident with plant transition from water to land	5
Comparative proteomic analysis of mitochondrial proteins from maize CMS‐C sterile, maintainer and restorer anthers	5
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	5
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	5
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks	5
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	5
Characterization of evolutionarily distinct rice BAHD‐Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani	5
Comparing gradient boosting machine and Bayesian threshold BLUP for genome‐based prediction of categorical traits in wheat breeding	4
Understanding the salt overly sensitive pathway in Prunus: Identification and characterization of NHX, CIPK, and CBL genes	4
Genetic control and allele variation among soybean maturity groups 000 through IX	4
Epigenetic regulation of photoperiodic flowering in plants	4
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	4
Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation	4
Machine learning approaches to identify core and dispensable genes in pangenomes	4
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	4
Subsampling and DNA pooling can increase gains through genomic selection in switchgrass	4
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	4
Genomic selection strategies to increase genetic gain in tea breeding programs	4
Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441	4
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice	4
What plant breeding may (and may not) look like in 2050?	4
Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection	4
Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	4
Changes in epigenetic features in legumes under abiotic stresses	4
Revealing the contribution of GbPR10.5D1 to resistance against Verticillium dahliae and its regulation for structural defense and immune signaling	4
Alfalfa genomic selection for different stress‐prone growing regions	4
Branch angle and leaflet shape are associated with canopy coverage in soybean	4
Lineage‐specific evolution of mangrove plastid genomes	4
Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding	4
Mineral nutrients in plants under changing environments: A road to future food and nutrition security	4
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	4
A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation	4
Bin mapping‐based QTL analyses using three genetic populations derived from indica–japonica crosses uncover multiple grain shape heterosis‐related loci in rice	4
A multi‐trait multi‐locus stepwise approach for conducting GWAS on correlated traits	4
Shaping the biology of citrus: I. Genomic determinants of evolution	4
Genetic dissection of seed characteristics in field pennycress via genome‐wide association mapping studies	4
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	4
Consensus genomic regions for grain quality traits in wheat revealed by Meta‐QTL analysis and in silico transcriptome integration	3
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	3
Meta‐QTL s and haplotypes for efficient zinc biofortification of rice	3
Genomic prediction of tocochromanols in exotic‐derived maize	3
Quantitative trait loci for yellow rust resistance in spring wheat doubled haploid populations developed from the German Federal ex situ genebank genetic resources	3
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds	3
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context	3
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	3
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	3
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	3
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	3
Mapping and validation of major and stable QTL for flag leaf size from tetraploid wheat	3
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity	3
Diversity of fatty acid biosynthesis genes across the soybean pangenome	3
Genomic‐assisted breeding for climate‐smart coffee	3
Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling	3
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat	3
Population structure and genetic diversity of U.S. wheat varieties	3
Combination of meta‐analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean	3
Genomic prediction for the Germplasm Enhancement of Maize project	3
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	3
New genomic regions associated with white mold resistance in dry bean using a MAGIC population	3
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	3
Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes	3
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	3
Genome‐wide identification and biological relevance of broccoli aquaporins	3
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	3
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability	3
Proteomic analysis of near‐isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance	3