Plant Genome

Papers
(The median citation count of Plant Genome is 2. 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 2021-05-01 to 2025-05-01.)
ArticleCitations
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP146
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola79
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress78
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters71
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis46
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling46
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador45
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication41
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 Caribbean34
The pangenome of banana highlights differences between genera and genomes33
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw32
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)32
TPG 2021 Publisher's Report30
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance29
Alfalfa genomic selection for different stress‐prone growing regions28
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars27
Genome‐wide association study of carotenoids in maize kernel26
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa24
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy24
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant23
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis23
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis23
Thanks to Our Reviewers, The Plant Genome, 202122
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy22
Recipients of 2020 CSSA Editor's Citation for Excellence Named21
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding21
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar‐S‐methyl20
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation20
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes20
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Shaping the biology of citrus: I. Genomic determinants of evolution19
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean19
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing19
Editorial Board19
Gain from genomic selection for a selection index in two‐row spring barley18
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds18
Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm18
Research highlights, The Plant Genome, Volume 14, Issue 218
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks18
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Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation18
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids17
Mutations in the dwarf3 gene confer height stability in sorghum17
Salinity stress tolerance prediction for biomass‐related traits in maize (Zea mays L.) using genome‐wide markers17
The Plant Genome special section: Modern improvement of tropical crops17
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Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding16
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A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits16
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame16
Machine learning approaches to identify core and dispensable genes in pangenomes16
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea15
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum15
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels15
Selection signatures in the CIMMYT International Elite Spring and Semi‐arid Wheat Yield Trials15
Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits14
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Genetic control of grain amino acid composition in a UK soft wheat mapping population14
Cover Image, Volume 15, Issue 214
A chromosome‐level genome of mango exclusively from long‐read sequence data14
Genes and genetic mechanisms contributing to fall armyworm resistance in maize14
Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding14
Erratum to: Fertilization of grapevine based on gene expression13
Common signatures of selection reveal target loci for breeding across soybean populations13
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains13
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)13
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species13
The conservation of gene models can support genome annotation13
Genetic control and allele variation among soybean maturity groups 000 through IX13
IGTCM: An integrative genome database of traditional Chinese medicine plants13
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association13
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum13
Accumulation of somatic mutations leads to genetic mosaicism in cannabis13
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi12
k‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel12
Issue Information12
Genomic and phenotypic characterization of finger millet indicates a complex diversification history12
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction12
Recipients of 2021 CSSA Editor's Citation for Excellence Named12
Research Highlights, The Plant Genome, Volume 15, Issue 412
An extensible vector toolkit and parts library for advanced engineering of plant genomes12
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa12
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools12
Genome‐wide association of dry (Tamar) date palm fruit color12
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)12
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana11
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 62211111
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant11
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits11
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials11
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks11
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley11
Deep‐learning power and perspectives for genomic selection11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses11
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program11
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study11
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement10
Diversity of cereal rye (Secale cereale) germplasm in the Southeast United States10
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations10
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga10
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias10
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change10
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES210
Insights into the roles of long noncoding RNAs in the communication between plants and the environment10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut10
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean9
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut9
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat9
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability9
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis9
Current technical advancements in plant epitranscriptomic studies9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed9
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits9
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea9
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence9
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat9
Systems biology for crop improvement9
Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance9
Genome‐wide identification and biological relevance of broccoli aquaporins9
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context9
Genome‐wide association study and KASP marker development for starch quality traits in wheat9
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean9
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize8
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat8
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat8
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR8
Validation of sorghum quality control (QC) markers across African breeding lines8
Genomic prediction of tocochromanols in exotic‐derived maize8
Diversity of fatty acid biosynthesis genes across the soybean pangenome8
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize8
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks8
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset8
Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa8
Genetic control of kernel compositional variation in a maize diversity panel8
Editorial Board8
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat8
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning8
Research highlights, The Plant Genome, Volume 16, Issue 48
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs8
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants8
Quantitative trait loci for yellow rust resistance in spring wheat doubled haploid populations developed from the German Federal ex situ genebank genetic resources8
Genomic prediction of seed nutritional traits in biparental families of oat (Avena sativa)7
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity7
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis7
Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication7
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)7
The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops7
k‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean7
Genomic and phenomic prediction for soybean seed yield, protein, and oil7
Environment characterization and genomic prediction for end‐use quality traits in soft white winter wheat7
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice7
Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative7
Erratum to “Identification, characterization, and expression of Oryza sativa tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolism”7
Haplotyping interspecific hybrids by dual alignment to both parental genomes7
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study7
Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD7
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing7
Shaping the biology of citrus: II. Genomic determinants of domestication7
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes6
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing6
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava6
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci6
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping6
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass6
Editorial Board6
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress6
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed6
RPAD locus controls prostrate growth habit in Oryza nivara6
Candidate selective sweeps in US wheat populations6
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis6
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding6
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain6
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat5
Thanks to Reviewers, The Plant Genome, 20235
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade5
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis5
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids5
Developing drought‐smart, ready‐to‐grow future crops5
Use of continuous genotypes for genomic prediction in sugarcane5
Editorial Board5
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis5
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials5
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research5
Genomic selection of parents and crosses beyond the native gene pool of a breeding program5
Maize and heat stress: Physiological, genetic, and molecular insights5
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection5
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)5
Generalizable approaches for genomic prediction of metabolites in plants5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits5
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon5
The economics and policy of genome editing in crop improvement4
Prospects for developing allergen‐depleted food crops4
Genomic selection of maize test‐cross hybrids leveraged by marker sampling4
Enhancing genomic‐based forward prediction accuracy in wheat by integrating UAV‐derived hyperspectral and environmental data with machine learning under heat‐stressed environments4
HaploCatcher: An R package for prediction of haplotypes4
Genomic‐assisted breeding for climate‐smart coffee4
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes4
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments4
A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage4
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Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat4
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa4
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives4
Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping4
Enhancing prediction accuracy of grain yield in wheat lines adapted to the southeastern United States through multivariate and multi‐environment genomic prediction models incorporating spectral and th4
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population4
Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi4
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes4
Research highlights, The Plant Genome, Volume 15, Issue 14
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat4
Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry4
Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger4
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines3
Validation of DNA marker‐assisted selection for forage biomass productivity under deficit irrigation in alfalfa3
Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm3
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean3
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize3
Introgression of genes associated with yield enhancement and resistance against bacterial leaf blight and blast diseases into an elite rice variety, Jaya3
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach3
DECUSSATEnetwork with flowering genes explains the variable effects ofqDTY12.1to rice yield under drought across genetic backgrounds3
Characterization of evolutionarily distinct rice BAHD‐Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani3
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Deep neural networks for genomic prediction do not estimate marker effects3
Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses3
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes3
Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 5664593
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program3
Cover Image, Volume 15, Issue 13
Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes3
Double‐digest restriction‐associated DNA sequencing‐based genotyping and its applications in sesame germplasm management3
High‐resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust3
Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment3
Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba3
Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain3
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar3
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Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection3
Genomic prediction for the Germplasm Enhancement of Maize project3
Evolutionary fates of gene‐body methylation and its divergent association with gene expression in pigeonpea3
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