Plant Genome

Article	Citations
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	149
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	82
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	78
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	50
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP	49
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	47
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	43
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	37
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	34
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	33
The pangenome of banana highlights differences between genera and genomes	32
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)	32
Alfalfa genomic selection for different stress‐prone growing regions	29
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	29
TPG 2021 Publisher's Report	29
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy	28
Genome‐wide association study of carotenoids in maize kernel	26
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	25
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	23
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	23
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	23
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar‐S‐methyl	22
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa	22
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	22
Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean (Lablab purpureus L. Sweet)	22

Thanks to Our Reviewers, The Plant Genome, 2021	22
Shaping the biology of citrus: I. Genomic determinants of evolution	21
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	20
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Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	20
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	20
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Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm	19
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Variant filters using segregation information improve mapping of nectar‐production genes in sunflower (Helianthus annuus L.)	19
Research highlights, The Plant Genome, Volume 14, Issue 2	19
The Plant Genome special section: Modern improvement of tropical crops	19
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	19
Editorial Board	19
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	19
Machine learning approaches to identify core and dispensable genes in pangenomes	18
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	18
Gain from genomic selection for a selection index in two‐row spring barley	18
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	18
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	18
Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation	18
Salinity stress tolerance prediction for biomass‐related traits in maize (Zea mays L.) using genome‐wide markers	18
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame	17
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds	17
Mutations in the dwarf3 gene confer height stability in sorghum	17
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	16
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Selection signatures in the CIMMYT International Elite Spring and Semi‐arid Wheat Yield Trials	16
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum	16
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	16
Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits	16
Genetic control of grain amino acid composition in a UK soft wheat mapping population	15
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	15
A chromosome‐level genome of mango exclusively from long‐read sequence data	15
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Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	14
Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding	14
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	14
Erratum to: Fertilization of grapevine based on gene expression	14
IGTCM: An integrative genome database of traditional Chinese medicine plants	14
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	14
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	14
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	14
Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2	14
Cover Image, Volume 15, Issue 2	14
Common signatures of selection reveal target loci for breeding across soybean populations	14
Genetic control and allele variation among soybean maturity groups 000 through IX	14
The conservation of gene models can support genome annotation	13

Research Highlights, The Plant Genome, Volume 15, Issue 4	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)	13
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	13
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)	13
An extensible vector toolkit and parts library for advanced engineering of plant genomes	13
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	13
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	13
Issue Information	13
Genome‐wide association of dry (Tamar) date palm fruit color	13
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	13
k‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	12
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	12
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	12
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	12
Recipients of 2021 CSSA Editor's Citation for Excellence Named	12
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant	12
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	12
Diversity of cereal rye (Secale cereale) germplasm in the Southeast United States	12
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	12
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	12
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	12
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	12
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	11
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	11
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks	11
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	11
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context	10
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	10
Deep‐learning power and perspectives for genomic selection	10
Genomic prediction in Persian walnut: Optimization levers according to genetic architecture of complex traits	10
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability	10
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean	10
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	10
Genome‐wide association study and KASP marker development for starch quality traits in wheat	10
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations	10
Genome‐wide identification and biological relevance of broccoli aquaporins	9
Editorial Board	9
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	9
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	9
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	9
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat	9
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat	9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	9
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	9
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	9
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	9
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	9
Current technical advancements in plant epitranscriptomic studies	9
Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	9
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut	9
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	9
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	9
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning	9
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	9
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger	9
Diversity of fatty acid biosynthesis genes across the soybean pangenome	8
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity	8
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	8
Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication	8
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	8
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize	8
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR	8
Research highlights, The Plant Genome, Volume 16, Issue 4	8
Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD	8
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	8
Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative	8
Validation of sorghum quality control (QC) markers across African breeding lines	8
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset	8
Genetic control of kernel compositional variation in a maize diversity panel	8
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	8
Genomic and phenomic prediction for soybean seed yield, protein, and oil	8
Environment characterization and genomic prediction for end‐use quality traits in soft white winter wheat	8
Genomic prediction of tocochromanols in exotic‐derived maize	8
Quantitative trait loci for yellow rust resistance in spring wheat doubled haploid populations developed from the German Federal ex situ genebank genetic resources	8

A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	7
Erratum to “Identification, characterization, and expression of Oryza sativa tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolism”	7
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	7
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	7
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice	7
Haplotyping interspecific hybrids by dual alignment to both parental genomes	7
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	7
Shaping the biology of citrus: II. Genomic determinants of domestication	7
Genomic prediction of seed nutritional traits in biparental families of oat (Avena sativa)	7
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	7
k‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	7
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	7
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	7
Use of continuous genotypes for genomic prediction in sugarcane	6
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis	6
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	6
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	6
Thanks to Reviewers, The Plant Genome, 2023	6
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	6
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing	6
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	6
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	6
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	6
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	6
RPAD locus controls prostrate growth habit in Oryza nivara	6
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	6
Developing drought‐smart, ready‐to‐grow future crops	6
Maize and heat stress: Physiological, genetic, and molecular insights	6
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	6
Editorial Board	6
Candidate selective sweeps in US wheat populations	6
Editorial Board	6
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	5
Research highlights, The Plant Genome, Volume 15, Issue 1	5
The economics and policy of genome editing in crop improvement	5
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Prospects for developing allergen‐depleted food crops	5
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat	5
Genomic‐assisted breeding for climate‐smart coffee	5
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)	5
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	5
Genomic selection of parents and crosses beyond the native gene pool of a breeding program	5
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	5
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	5
Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry	5
Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat	5
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives	5
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	5
Generalizable approaches for genomic prediction of metabolites in plants	5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns	5
A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage	5
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes	5
Enhancing genomic‐based forward prediction accuracy in wheat by integrating UAV‐derived hyperspectral and environmental data with machine learning under heat‐stressed environments	5
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa	5
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	5
HaploCatcher: An R package for prediction of haplotypes	5
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Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi	5
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	4
Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping	4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	4
Deep neural networks for genomic prediction do not estimate marker effects	4
Evaluation of eight Bayesian genomic prediction models for three micronutrient traits in bread wheat (Triticum aestivum L.)	4
Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba	4
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	4
Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study	4
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program	4
Cover Image, Volume 15, Issue 1	4
New genomic regions associated with white mold resistance in dry bean using a MAGIC population	4
Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry	4
Introgression of genes associated with yield enhancement and resistance against bacterial leaf blight and blast diseases into an elite rice variety, Jaya	4
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean	4
Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection	4
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 th	4
Validation of DNA marker‐assisted selection for forage biomass productivity under deficit irrigation in alfalfa	4
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	4
Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459	4
Training set design in genomic prediction with multiple biparental families	3
Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing	3
Genetic architecture of anthocyanin pigment traits and purple spot (Stemphylium vesicarium) resistance in an F1 pseudo‐testcross population of asparagus	3
Soybean genomics research community strategic plan: A vision for 2024–2028	3
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	3
Subsampling and DNA pooling can increase gains through genomic selection in switchgrass	3
Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry	3
Genomic prediction for the Germplasm Enhancement of Maize project	3
DECUSSATEnetwork with flowering genes explains the variable effects ofqDTY12.1to rice yield under drought across genetic backgrounds	3
Genetic basis for lentil adaptation to summer cropping in northern temperate environments	3
Editorial Board	3