Plant Genome

Article	Citations
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	175
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	82
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	45
Chromosome‐level genome of Zoysia sinica in the intertidal zone reveals genomic insights into waterlogging stress adaptation	44
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem du	43
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	42
Genetic control of root architectural traits under drought stress in spring barley ( Hordeum vulgare L.)	37
Genetic dissection of the root system architecture QTLome and its relationship with early shoot development, breeding and adaptation in durum wheat	36
TPG 2021 Publisher's Report	35
Correction to “Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato”	35
A chickpea MAGIC population to dissect the genetics of complex traits	32
Trait mapping differentiates loci influencing spike and flag leaf glaucousness in wheat	32
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	31
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	30
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	30
Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean ( Lablab purpureus	30
Alfalfa genomic selection for different stress‐prone growing regions	29
Genome‐wide association study of carotenoids in maize kernel	29
Genomic and biochemical comparison of allelic triple‐mutant lines derived from conventional breeding and multiplex gene editing	29
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	29
Targets and strategies to design soybean seed composition traits	28
Correction to “Genome‐wide association study identifies QTL and candidate genes for grain size and weight in a Triticum turgidum collection”	27
A novel allele of Days to Heading 8 promotes heading, potentially widening indica rice adaptation in Japan	26
Transcript profiling of hairy vetch ( Vicia villosa Roth) identified interesting genes for seed dormancy	24
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium<	24

Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora	23
Variant filters using segregation information improve mapping of nectar‐production genes in sunflower ( Helianthus annuus L.)	23
Decoding the CBL gene family in durum wheat: Insights into dual ABA signaling pathways and calcium‐mediated drought tolerance	23
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	23
Thanks to Our Reviewers, The Plant Genome , 2021	22
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Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	21
Genome‐wide association studies reveal genetic control of nutritional quality, milling traits, and agronomic characteristics in oat ( Avena sativa L.)	21
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	21
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Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	20
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds	20
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	20
The Plant Genome special section: Modern improvement of tropical crops	18
Optimizing genomic prediction with transfer learning under a ridge regression framework	18
Salinity stress tolerance prediction for biomass‐related traits in maize ( Zea mays L.) using genome‐wide markers	18
Integration of physiological and remote sensing traits for improved genomic prediction of wheat yield	18
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Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm	18
Mutations in the dwarf3 gene confer height stability in sorghum	18
Editorial Board	18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	17
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	17
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame	17
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	17
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Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes	16
Diverse reference genomes detect variants in the US winter wheat	16
Analysis of candidate genes identified via genome‐wide association analysis of sugar‐related traits in maize kernels	16
Genome‐wide association study of seed mineral nutrients in peas ( Pisum sativum L.)	16
A chromosome‐level genome of mango exclusively from long‐read sequence data	16
Genetic control of grain amino acid composition in a UK soft wheat mapping population	16
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	15
Erratum to: Fertilization of grapevine based on gene expression	15
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum	15
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	15
The conservation of gene models can support genome annotation	15
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	15
Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits	15
Erratum to “Alanine aminotransferase contributes to hypoxia sensitivity and dormancy in barley seeds”	15
Common signatures of selection reveal target loci for breeding across soybean populations	14
Multi‐trait/environment sparse genomic prediction using the SFSI R‐package	14
Cover Image, Volume 15, Issue 2	14
IGTCM: An integrative genome database of traditional Chinese medicine plants	14
Chromosome‐level genome assembly of Indian mangrove ( Ceriops tagal ) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae	14
Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy	14
Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2	14
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	14
Integrated chloroplast genomics and whole‐genome resequencing reveals demographic history and selection signatures of black walnuts	13
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	13

Editorial Board	13
MicroRNAs‐mediated heat stress regulations in plants: Mechanisms and targets	13
Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean	13
The Plant Genome Annual Report, 2024	13
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat ( Triticum aestivum L.)	13
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	12
Issue Information	12
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat ( Triticum aestivum	12
Diversity of cereal rye ( Secale cereale ) germplasm in the Southeast United States	12
Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phy	12
Genome‐wide association of dry (Tamar) date palm fruit color	12
An extensible vector toolkit and parts library for advanced engineering of plant genomes	12
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	12
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	12
Pangenome insights into structural variation and functional diversification of barley CCT motif genes	12
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	12
Research Highlights, The Plant Genome , Volume 15, Issue 4	12
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant	12
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	12
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata : Protein‐coding genes, microRNAs, and regulatory networks	11
Recipients of 2021 CSSA Editor's Citation for Excellence Named	11
Development of functional markers and expression analysis for a Peroxidase gene TaPod‐A3 on chromosome 7AL in wheat	11
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	11
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	11
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	11
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	11
Seed protein electrophoresis in plant genetics: Commemorating the pioneering contributions of Prof. Chittaranjan Kole and team to the foundation of plant proteomics	11
k ‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	11
Genetic mapping of a chickpea ( Cicer arietinum L.) diversity panel for mineral biofortification towards human nutrition	11
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	11
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	11
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	11
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Genomic prediction in Persian walnut: Optimization levers according to genetic architecture of complex traits	11
Genome‐wide association study and KASP marker development for starch quality traits in wheat	10
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	10
Genomic selection: Essence, applications, and prospects	10
Genomic selection of soybean ( Glycine max ) for genetic improvement of yield and seed composition in a breeding context	10
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	10
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	10
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean	10
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat	10
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	10
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	10
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	9
The PIN2 ortholog in barley modifies root gravitropism and architecture	9
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	9
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning	9
Genome‐wide identification and biological relevance of broccoli aquaporins	9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	9
Enhancing prediction accuracy of key biomass partitioning traits in wheat using multi‐kernel genomic prediction models integrating secondary traits and environmental covariates	9
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat	9
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity	9
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut	9
Current technical advancements in plant epitranscriptomic studies	9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	9
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	9
Distinct classes of 21‐ and 24‐nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development	9
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger	9
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	9
Genetic variation in a tepary bean ( Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	9
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	9
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Identification and mapping of quantitative trait loci for Fusarium head blight resistance in a synthetic hexaploid × hard red spring wheat population	8
Editorial Board	8
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR	8
Diversity of fatty acid biosynthesis genes across the soybean pangenome	8
Machine learning‐driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao	8
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	8
Environment ensemble models for genomic prediction in common bean ( Phaseolus vulgaris L.)	8
Validation of sorghum quality control (QC) markers across African breeding lines	8
Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato	8
Research highlights, The Plant Genome , Volume 16, Issue 4	8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset	8
Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize	8
Genomic prediction of tocochromanols in exotic‐derived maize	8
Haplotyping interspecific hybrids by dual alignment to both parental genomes	8
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	7

Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication	7
A view of the pan‐genome of domesticated Cowpea ( Vigna unguiculata [L.] Walp.)	7
Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative	7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	7
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	7
Haplotype‐based insights into seminal root angle in barley	7
Genomic and phenomic prediction for soybean seed yield, protein, and oil	7
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice	7
A low‐coverage skim‐sequencing and imputation pipeline for genomic selection	7
k ‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Assessing genetic diversity and performing genome‐wide association studies (GWAS) using multiple marker types across desi, kabuli, and wild accessions in chickpea ( Cicer arieti	7
Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement	7
Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD	7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	7
Enhancing crop resilience through elite pre‐breeding lines with key traits for dry direct‐seeded rice	7
Genomic prediction of seed nutritional traits in biparental families of oat ( Avena sativa )	6
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Candidate selective sweeps in US wheat populations	6
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	6
RPAD locus controls prostrate growth habit in Oryza nivara	6
The Big BIT maize experiment: A large multi‐location, multi‐year, multi‐tester, multi‐population predictive breeding validation study	6
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	6
Crop growth model‐enabled genetic mapping of biomass accumulation dynamics in photoperiod‐sensitive sorghum	6
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing	6
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	6
Editorial Board	6
Use of continuous genotypes for genomic prediction in sugarcane	6
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	6
Erratum to “Identification, characterization, and expression of  Oryza sativa  tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolis	6
Thanks to Reviewers, The Plant Genome , 2023	6
Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato ( Solanum tuberosum )	6
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	6
Editorial Board	6
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	5
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Editorial Board	5
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	5
Developing drought‐smart, ready‐to‐grow future crops	5
Generalizable approaches for genomic prediction of metabolites in plants	5
Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi	5
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	5
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	5
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	5
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns	5
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	5
Phenotypic plasticity in maize grain yield: Genetic and environmental insights of response to environmental gradients	5
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	5
Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole‐genome resequence and multi‐environmental data	5
Harnessing genomic prediction in Brassica napus through a nested association mapping population	5
Maize and heat stress: Physiological, genetic, and molecular insights	5
New genomic resources to boost research in reproductive biology to enable cost‐effective hybrid seed production	5
A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage	4
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	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
Understanding the genetic basis of heat stress tolerance in wheat ( Triticum aestivum L.) through genome‐wide association studies	4
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	4
The economics and policy of genome editing in crop improvement	4
Enhancing genomic‐based forward prediction accuracy in wheat by integrating UAV‐derived hyperspectral and environmental data with machine learning under heat‐stressed environments	4
Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat	4
HaploCatcher: An R package for prediction of haplotypes	4
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	4
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	4
Hybrid kernels integrating genomic and multispectral data improve wheat genomic prediction accuracy	4
Research highlights, The Plant Genome , Volume 15, Issue 1	4
Genetic mapping and haplotype analysis identify novel candidate genes for high night temperature tolerance in winter wheat	4
Genomic‐assisted breeding for climate‐smart coffee	4
Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry	4
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	4
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat	4
Prospects for developing allergen‐depleted food crops	4
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	4
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	4
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Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping	4
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CRISPR‐induced knockouts reveal a dual role for the soybean NFR5α gene in symbiotic nitrogen fixation and root hair development	4
Insights into the genetic and biochemical basis of Gibberella ear rot resistance in maize	4
Genome‐wide association study and molecular marker development for resistance to soybean cyst nematode in soybean	4
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Came	4
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives	4
Genomic prediction for potato ( Solanum tuberosum ) quality traits improved through image analysis	4
The role of microRNAs in responses to drought and heat stress in peanut ( Arachis hypogaea )	4
Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459	3
Cover Image, Volume 15, Issue 1	3
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	3
Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm	3
Effects of SNP marker density and training population size on prediction accuracy in alfalfa ( Medicago sativa L.) genomic selection	3
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	3
Identification of a genomic region containing genes involved in resistance to four pathotypes of Plasmodiophora brassicae in Brass	3
RADseq‐based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna	3
Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain	3
Genomic prediction for heat and herbicide tolerance in faba bean	3
Phenome‐to‐genome insights for evaluating root system architecture in field studies of maize	3