Plant Genome

Article	Citations
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	117
Genomic prediction of seed nutritional traits in biparental families of oat (Avena sativa)	62
Integrating de novo QTL‐seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean	61
Genomic prediction for the Germplasm Enhancement of Maize project	60
Identifying and expression analysis of WD40 transcription factors in walnut	41
Research Highlights, The Plant Genome, Volume 15, Issue 4	39
Thanks to Reviewers, The Plant Genome, 2022	37
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	32
Issue Information	28
Shaping the biology of citrus: II. Genomic determinants of domestication	26
DECUSSATEnetwork with flowering genes explains the variable effects ofqDTY12.1to rice yield under drought across genetic backgrounds	25
The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation	24
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The soybean ubiquitin‐proteasome system: Current knowledge and future perspective	24
Characterization of evolutionarily distinct rice BAHD‐Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani	23
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP	23
Cover Image, Volume 14, Issue 2	22
Research highlights, The Plant Genome, Volume 16, Issue 3	20
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	20
Evolutionary fates of gene‐body methylation and its divergent association with gene expression in pigeonpea	20
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	20
Integrated multi‐omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.)	19
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	18
Approaches and progress in breeding drought‐tolerant maize hybrids for tropical lowlands in west and central Africa	18
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	18

An extensible vector toolkit and parts library for advanced engineering of plant genomes	17
Editorial Board	16
RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat	16
Genetic architecture of protein and oil content in soybean seed and meal	16
Differentially expressed microRNAs that target functional genes in mature soybean nodules	16
Identification and assessment of alleles in the promoter of the Cyc‐B gene that modulate levels of β‐carotene in ripe tomato fruit	16
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	16
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	15
Antimicrobial peptides in Dendrobium officinale: Genomic parameters, peptide structures, and gene expression patterns	15
Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose	15
Genomic selection strategies to increase genetic gain in tea breeding programs	15
Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents	15
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	15
Training set design in genomic prediction with multiple biparental families	14
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	14
Consensus genomic regions for grain quality traits in wheat revealed by Meta‐QTL analysis and in silico transcriptome integration	14
Genetic dissection of domestication traits in interspecific chickpea populations	14
Genome‐wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments	14
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	14
High‐resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust	13
Genomic selection optimization in blueberry: Data‐driven methods for marker and training population design	13
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	13
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	13
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	13
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	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)	13
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	13
The trans‐kingdom communication of noncoding RNAs in plant–environment interactions	13
Branch angle and leaflet shape are associated with canopy coverage in soybean	13
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	13
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	13
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	13
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	13
Increasing the level of resistant starch in ‘Presidio’ rice through multiplex CRISPR–Cas9 gene editing of starch branching enzyme genes	12
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)	12
Genome‐wide association of dry (Tamar) date palm fruit color	12
Comparing gradient boosting machine and Bayesian threshold BLUP for genome‐based prediction of categorical traits in wheat breeding	12
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	12
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	12
Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization	12
The pangenome of banana highlights differences between genera and genomes	12
Development of whole‐genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding	12
Using cross‐country datasets for association mapping in Arachis hypogaea L.	12
Development and evaluation of Fusarium wilt‐resistant and high‐yielding chickpea advanced breeding line, KCD 11	12
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	11
Genetic dissection of seed characteristics in field pennycress via genome‐wide association mapping studies	11
Combining genome‐wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot	11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Combination of meta‐analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean	11
Cover Image, Volume 14, Issue 3	11

Use of continuous genotypes for genomic prediction in sugarcane	11
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	11
Introducing CHiDO—A No Code Genomic Prediction software implementation for the characterization and integration of driven omics	11
Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks	11
Focusing the GWAS Lens on days to flower using latent variable phenotypes derived from global multienvironment trials	10
The Plant Genome special section: Grain quality and nutritional genomics for breeding next‐generation crops	10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	10
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	10
Alfalfa genomic selection for different stress‐prone growing regions	10
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	10
Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans	10
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	10
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	10
Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing	10
Genome‐wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes	10
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa	10
Maize and heat stress: Physiological, genetic, and molecular insights	10
Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China	10
Recipients of 2021 CSSA Editor's Citation for Excellence Named	9
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	9
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	9
TPG 2021 Publisher's Report	9
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	9
Issue Information	9
Subsampling and DNA pooling can increase gains through genomic selection in switchgrass	9
Proteomic analysis of near‐isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance	9
Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations	9
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks	9
Analysis of the primary sources of quantitative adult plant resistance to stripe rust in U.S. soft red winter wheat germplasm	9
Research highlights, The Plant Genome, Volume 16, Issue 2	9
Thanks to Reviewers, The Plant Genome, 2023	8
Integration of machine learning and genome‐wide association study to explore the genomic prediction accuracy of agronomic trait in oats (Avena sativa L.)	8
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	8
Genome‐wide association study for yield and quality of granulated cassava processed product	8
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing	8
Simulations of multiple breeding strategy scenarios in common bean for assessing genomic selection accuracy and model updating	8
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	8
Genomic variation within the maize stiff‐stalk heterotic germplasm pool	8
Genome assembly and multi‐omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri	8
Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry	8
Critical roles of the activation of ethylene pathway genes mediated by DNA demethylation in Arabidopsis hyperhydricity	8
Transcriptome‐wide expression landscape and starch synthesis pathway co‐expression network in sorghum	8
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	8
Leveraging spatiotemporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models	8
Editorial Board	8
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	8
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	8
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	7
Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback	7
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	7
Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress	7
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy	7
Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene	7
Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR	7
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	7
Genome‐wide association of an organic naked barley diversity panel identified quantitative trait loci for disease resistance	7
k‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	7
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	7
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	7
Genetic dissection of maize plant architecture using a novel nested association mapping population	7
Editorial Board	7
The application of pangenomics and machine learning in genomic selection in plants	7
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	7
Soybean genomics research community strategic plan: A vision for 2024–2028	7
A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis	7
Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome‐wide association study	7
Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life	7
Candidate selective sweeps in US wheat populations	7
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	6
A medium‐density genotyping platform for cultivated strawberry using DArTag technology	6
Genome‐wide analysis of HD‐Zip genes in Sophora alopecuroides and their role in salt stress response	6
Research highlights, The Plant Genome, Volume 15, Issue 2	6
Research highlights, The Plant Genome, Volume 14, Issue 1	6
Revealing the contribution of GbPR10.5D1 to resistance against Verticillium dahliae and its regulation for structural defense and immune signaling	6
Deep‐learning power and perspectives for genomic selection	6
Developing drought‐smart, ready‐to‐grow future crops	6
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	6
Skim exome capture genotyping in wheat	6
Cover Image, Volume 14, Issue 1	6
Identification and evolutionary analysis of the metal‐tolerance protein family in eight Cucurbitaceae species	6

Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust	6
Genome‐wide association study of carotenoids in maize kernel	6
Genome‐wide association study identifies QTL and candidate genes for grain size and weight in a Triticum turgidum collection	6
Recipients of 2020 CSSA Editor's Citation for Excellence Named	6
Thanks to our reviewers, The Plant Genome, 2020	6
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	5
Differential gene expression in tall fescue tissues in response to water deficit	5
Genomic selection of parents and crosses beyond the native gene pool of a breeding program	5
Thanks to Our Reviewers, The Plant Genome, 2021	5
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Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	5
Genomic‐wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids	5
Chromosome‐scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression	5
GEPSdb: The Gene Expression Database of Poplar under Stress	5
Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry	5
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations	5
Genome‐wide association study and KASP marker development for starch quality traits in wheat	5
Identification and mapping of QTLs and their corresponding candidate genes controlling high night‐time temperature stress tolerance in wheat (Triticum aestivum L.)	5
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)	5
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	5
Integrated meta‐QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.)	5
Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time	5
Genetic resources and genes/QTLs for gram pod borer (Helicoverpa armigera Hübner) resistance in chickpea from the Western Himalayas	5
Cover Image, Volume 15, Issue 4	5
Genomic prediction for complex traits across multiples harvests in alfalfa (Medicago sativa L.) is enhanced by enviromics	5
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Integration of metabolomics and transcriptomics data to further characterize Gliricidia sepium (Jacq.) Kunth under high salinity stress	5
Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458	5
Imputation of low‐density marker chip data in plant breeding: Evaluation of methods based on sugar beet	5
Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi	5
Shaping the biology of citrus: I. Genomic determinants of evolution	4
Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize	4
Dynamic changes of genome sizes and gradual gain of cell‐specific distribution of C4 enzymes during C4 evolution in genus Flaveria	4
Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL	4
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	4
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	4
Sparse multi‐trait genomic prediction under balanced incomplete block design	4
The Plant Genome special section: Epigenome and epitranscriptome in plant–environment interactions	4
Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping	4
Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa	4
Single‐nucleotide mosaicism in citrus: Estimations of somatic mutation rates and total number of variants	4
Adult plant leaf rust resistance QTL derived from wheat line CI13227 maps to chromosomes 2AL, 4BS, and 7AL	4
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	4
Genome‐wide identification and functional profile analysis of long non‐coding RNAs in Avicennia marina	4
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	4
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat	4
ASRpro: A machine‐learning computational model for identifying proteins associated with multiple abiotic stress in plants	4
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	4
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	4
Understanding role of roots in plant response to drought: Way forward to climate‐resilient crops	4
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	4
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	4
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	4
A review of plant epigenetics through the lens of almond	4
Genome‐wide identification and expression analysis of heat shock protein gene family in cassava	4
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	3
Generalizable approaches for genomic prediction of metabolites in plants	3
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat	3
Characterization and regulatory mechanism analysis of VvmiR156a–VvAGL80 pair during grapevine flowering and parthenocarpy process induced by gibberellin	3
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	3
Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program	3
Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions	3
Association study of crude seed protein and fat concentration in a USDA pea diversity panel	3
Population structure and genetic diversity of U.S. wheat varieties	3
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	3
ERRATUM: Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization	3
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	3
Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce	3
Within‐family genomic selection in strawberry: Optimization of marker density, trial design, and training set composition	3
Genome‐wide association mapping reveals novel genes and genomic regions controlling root‐lesion nematode resistance in chickpea mini core collection	3
A multi‐trait multi‐locus stepwise approach for conducting GWAS on correlated traits	3
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context	3
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	3
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis	3
Whole‐genome versus per‐chromosome targeted recombination: Simulations and predicted gains in maize with an integer programming model	3
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	3
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability	3
Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis	3
Association mapping and genomic prediction for processing and end‐use quality traits in wheat (Triticum aestivum L.)	3
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	2
The Plant Genome special section: Modern improvement of tropical crops	2
Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling	2
Genome‐wide SNP discovery and genotyping delineates potential QTLs underlying major yield‐attributing traits in buckwheat	2
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat	2
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	2
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Integrated transcriptomic and lipidomic analysis provides key insights into lipid content changes during pecan (Carya illinoensis) fruit development	2
Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar	2
Research highlights, The Plant Genome, Volume 14, Issue 2	2
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	2
Research highlights, The Plant Genome, Volume 15, Issue 1	2
Genetic loci regulating the concentrations of anthocyanins and proanthocyanidins in the pericarps of purple and red rice	2
Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat	2
Transcriptome profiling reveals the expression and regulation of genes associated with Fusarium wilt resistance in chickpea (Cicer arietinum L.)	2
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	2