Plant Genome

Article	Citations
Chromosome‐level genome of Zoysia sinica in the intertidal zone reveals genomic insights into waterlogging stress adaptation	164
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP	89
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	61
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	52
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	39
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	38
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	37
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	33
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)	33
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	33
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	32
Genomic and biochemical comparison of allelic triple‐mutant lines derived from conventional breeding and multiplex gene editing	30
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	30
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	30
Alfalfa genomic selection for different stress‐prone growing regions	28
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	27
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa	27
Trait mapping differentiates loci influencing spike and flag leaf glaucousness in wheat	27
TPG 2021 Publisher's Report	26
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy	25
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	24
Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean (Lablab purpureus L. Sweet)	24
Genome‐wide association study of carotenoids in maize kernel	23
A chickpea MAGIC population to dissect the genetics of complex traits	23
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	22

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Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	22
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	22
Genome‐wide association studies reveal genetic control of nutritional quality, milling traits, and agronomic characteristics in oat (Avena sativa L.)	22
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	21
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar‐S‐methyl	21
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	21
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	20
Variant filters using segregation information improve mapping of nectar‐production genes in sunflower (Helianthus annuus L.)	20
Decoding the CBL gene family in durum wheat: Insights into dual ABA signaling pathways and calcium‐mediated drought tolerance	20
Thanks to Our Reviewers, The Plant Genome, 2021	20
The Plant Genome special section: Modern improvement of tropical crops	19
Gain from genomic selection for a selection index in two‐row spring barley	19
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A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	19
Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes	19
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Editorial Board	19
Salinity stress tolerance prediction for biomass‐related traits in maize (Zea mays L.) using genome‐wide markers	19
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	18
Mutations in the dwarf3 gene confer height stability in sorghum	18
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds	18
Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm	18
Machine learning approaches to identify core and dispensable genes in pangenomes	18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	17
Optimizing genomic prediction with transfer learning under a ridge regression framework	17
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame	17
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Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	17
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum	16
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	16
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels	16
Genetic control of grain amino acid composition in a UK soft wheat mapping population	16
Selection signatures in the CIMMYT International Elite Spring and Semi‐arid Wheat Yield Trials	16
A chromosome‐level genome of mango exclusively from long‐read sequence data	16
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
The conservation of gene models can support genome annotation	15
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	15
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	15
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Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding	15
IGTCM: An integrative genome database of traditional Chinese medicine plants	14
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	14
Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species	14
Erratum to: Fertilization of grapevine based on gene expression	14
Cover Image, Volume 15, Issue 2	14
Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy	13
Genetic control and allele variation among soybean maturity groups 000 through IX	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)	13

Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phytophthora sojae in soybean	13
Genome‐wide association of dry (Tamar) date palm fruit color	13
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	13
Multi‐trait/environment sparse genomic prediction using the SFSI R‐package	13
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)	13
Research Highlights, The Plant Genome, Volume 15, Issue 4	13
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	13
Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2	13
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	13
Common signatures of selection reveal target loci for breeding across soybean populations	13
Issue Information	13
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	13
An extensible vector toolkit and parts library for advanced engineering of plant genomes	12
Pangenome insights into structural variation and functional diversification of barley CCT motif genes	12
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	12
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	12
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	12
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant	11
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	11
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	11
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	11
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	11
Diversity of cereal rye (Secale cereale) germplasm in the Southeast United States	11
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials	11
An organ‐specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein‐coding genes, microRNAs, and regulatory networks	11
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	11
k‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	11
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	10
Seed protein electrophoresis in plant genetics: Commemorating the pioneering contributions of Prof. Chittaranjan Kole and team to the foundation of plant proteomics	10
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context	10
Genomic selection: Essence, applications, and prospects	10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	10
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	10
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	10
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	10
Genome‐wide association study and KASP marker development for starch quality traits in wheat	10
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean	10
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations	10
Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga	10
Recipients of 2021 CSSA Editor's Citation for Excellence Named	10
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	10
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability	10
Genomic prediction in Persian walnut: Optimization levers according to genetic architecture of complex traits	10
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat	10
Development of functional markers and expression analysis for a Peroxidase gene TaPod‐A3 on chromosome 7AL in wheat	10
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	9
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	9
Current technical advancements in plant epitranscriptomic studies	9
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	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 analysis of spike and kernel traits in the U.S. hard winter wheat	9
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	9
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger	9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	9
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat	9
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	9
Genome‐wide identification and biological relevance of broccoli aquaporins	9
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning	9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut	9
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	9
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	8
Validation of sorghum quality control (QC) markers across African breeding lines	8
Diversity of fatty acid biosynthesis genes across the soybean pangenome	8
Identification and mapping of quantitative trait loci for Fusarium head blight resistance in a synthetic hexaploid × hard red spring wheat population	8
Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	8
The PIN2 ortholog in barley modifies root gravitropism and architecture	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
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
Editorial Board	8
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset	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
Genomic prediction of tocochromanols in exotic‐derived maize	8
Research highlights, The Plant Genome, Volume 16, Issue 4	8
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	8
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	8

Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative	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
A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)	7
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	7
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	7
Erratum to “Identification, characterization, and expression of Oryza sativa tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolism”	7
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	7
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	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
Machine learning‐driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao	7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	7
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	7
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	7
Haplotype‐based insights into seminal root angle in barley	7
k‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	7
Haplotyping interspecific hybrids by dual alignment to both parental genomes	7
Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.)	7
Genomic prediction of seed nutritional traits in biparental families of oat (Avena sativa)	7
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	7
Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication	7
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	6
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	6
Developing drought‐smart, ready‐to‐grow future crops	6
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	6
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	6
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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
Maize and heat stress: Physiological, genetic, and molecular insights	6
Thanks to Reviewers, The Plant Genome, 2023	6
Candidate selective sweeps in US wheat populations	6
RPAD locus controls prostrate growth habit in Oryza nivara	6
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing	6
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	6
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Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	6
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	6
Editorial Board	6
Editorial Board	6
Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato (Solanum tuberosum)	6
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns	5
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)	5
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa	5
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	5
Genome‐wide association study and molecular marker development for resistance to soybean cyst nematode in soybean	5
Research highlights, The Plant Genome, Volume 15, Issue 1	5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	5
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	5
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	5
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis	5
Phenotypic plasticity in maize grain yield: Genetic and environmental insights of response to environmental gradients	5
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	5
Insights into the genetic and biochemical basis of Gibberella ear rot resistance in maize	5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	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 parents and crosses beyond the native gene pool of a breeding program	5
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	5
New genomic resources to boost research in reproductive biology to enable cost‐effective hybrid seed production	5
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Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	5
Genomic‐assisted breeding for climate‐smart coffee	4
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives	4
Prospects for developing allergen‐depleted food crops	4
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	4
Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping	4
Understanding the genetic basis of heat stress tolerance in wheat (Triticum aestivum L.) through genome‐wide association studies	4
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes	4
Cover Image, Volume 15, Issue 1	4
A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage	4
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat	4
Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry	4
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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
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	4
Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study	4
Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat	4
The economics and policy of genome editing in crop improvement	4
HaploCatcher: An R package for prediction of haplotypes	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
Genetic mapping and haplotype analysis identify novel candidate genes for high night temperature tolerance in winter wheat	4
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	4
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean	4
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	3
Deep neural networks for genomic prediction do not estimate marker effects	3
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	3
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Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm	3
Phenome‐to‐genome insights for evaluating root system architecture in field studies of maize	3