Plant Genome

Article	Citations
Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α‐SNAP	146
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	79
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	78
Genomic prediction modeling of soybean biomass using UAV‐based remote sensing and longitudinal model parameters	71
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis	46
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	46
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	45
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication	41
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	34
The pangenome of banana highlights differences between genera and genomes	33
Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw	32
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)	32
TPG 2021 Publisher's Report	30
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	29
Alfalfa genomic selection for different stress‐prone growing regions	28
Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars	27
Genome‐wide association study of carotenoids in maize kernel	26
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa	24
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	24
The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis	23
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	23
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	23
Transcript profiling of hairy vetch (Vicia villosaRoth) identified interesting genes for seed dormancy	22
Thanks to Our Reviewers, The Plant Genome, 2021	22
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding	21

Recipients of 2020 CSSA Editor's Citation for Excellence Named	21
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes	20
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar‐S‐methyl	20
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	20
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	19
Editorial Board	19
	19
	19
Shaping the biology of citrus: I. Genomic determinants of evolution	19
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	19
Gain from genomic selection for a selection index in two‐row spring barley	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
Research highlights, The Plant Genome, Volume 14, Issue 2	18
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	18
	18
Positional‐based cloning ‘fail‐safe’ approach is overpowered by wheat chromosome structural variation	18
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids	17
Mutations in the dwarf3 gene confer height stability in sorghum	17
Salinity stress tolerance prediction for biomass‐related traits in maize (Zea mays L.) using genome‐wide markers	17
The Plant Genome special section: Modern improvement of tropical crops	17
Machine learning approaches to identify core and dispensable genes in pangenomes	16
	16
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	16
	16
A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits	16
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame	16
Selection signatures in the CIMMYT International Elite Spring and Semi‐arid Wheat Yield Trials	15
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	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
A chromosome‐level genome of mango exclusively from long‐read sequence data	14
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	14
Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding	14
Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits	14
	14
Genetic control of grain amino acid composition in a UK soft wheat mapping population	14
Cover Image, Volume 15, Issue 2	14
Accumulation of somatic mutations leads to genetic mosaicism in cannabis	13
Erratum to: Fertilization of grapevine based on gene expression	13
Common signatures of selection reveal target loci for breeding across soybean populations	13
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	13
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 species	13
The conservation of gene models can support genome annotation	13
Genetic control and allele variation among soybean maturity groups 000 through IX	13
IGTCM: An integrative genome database of traditional Chinese medicine plants	13
Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association	13
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	13

Genome‐wide association of dry (Tamar) date palm fruit color	12
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.)	12
Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi	12
k‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	12
Issue Information	12
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	12
Application of a Poisson deep neural network model for the prediction of count data in genome‐based prediction	12
Recipients of 2021 CSSA Editor's Citation for Excellence Named	12
Research Highlights, The Plant Genome, Volume 15, Issue 4	12
An extensible vector toolkit and parts library for advanced engineering of plant genomes	12
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	12
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	12
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	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
Deep‐learning power and perspectives for genomic selection	11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	11
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	11
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	11
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	11
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	11
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant	11
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	10
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	10
Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad‐spectrum resistance	10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	10
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	10
The Plant Genomespecial issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement	10
Diversity of cereal rye (Secale cereale) germplasm in the Southeast United States	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
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	9
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	9
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence	9
Deciphering the genetic basis of novel traits that discriminate useful and non‐useful biomass to enhance harvest index in wheat	9
Systems biology for crop improvement	9
Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	9
Genome‐wide identification and biological relevance of broccoli aquaporins	9
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context	9
Genome‐wide association study and KASP marker development for starch quality traits in wheat	9
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean	9
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	9
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut	9
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	9
Optimizing the setup of multienvironmental hybrid wheat yield trials for boosting the selection capability	9
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	9
Current technical advancements in plant epitranscriptomic studies	9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	9
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger	8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset	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
Genetic control of kernel compositional variation in a maize diversity panel	8
Editorial Board	8
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat	8
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning	8
Research highlights, The Plant Genome, Volume 16, Issue 4	8
Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs	8
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants	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
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	8
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	8
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR	8
Validation of sorghum quality control (QC) markers across African breeding lines	8
Genomic prediction of tocochromanols in exotic‐derived maize	8
Diversity of fatty acid biosynthesis genes across the soybean pangenome	8
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize	8
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	8
k‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Genomic and phenomic prediction for soybean seed yield, protein, and oil	7
Environment characterization and genomic prediction for end‐use quality traits in soft white winter wheat	7
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice	7
Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative	7
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 genomes	7
Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study	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
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
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity	7
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	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
The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation	7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	7
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	6
Editorial Board	6
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	6
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	6
RPAD locus controls prostrate growth habit in Oryza nivara	6
Candidate selective sweeps in US wheat populations	6
Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis	6
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding	6
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	6
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	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
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	6
Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping	6
Developing drought‐smart, ready‐to‐grow future crops	5
Use of continuous genotypes for genomic prediction in sugarcane	5
Editorial Board	5
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis	5
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	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
Maize and heat stress: Physiological, genetic, and molecular insights	5
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	5
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)	5
Generalizable approaches for genomic prediction of metabolites in plants	5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	5
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
Multi‐trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat	5
Thanks to Reviewers, The Plant Genome, 2023	5
Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade	5
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	5
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns	5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	5
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	4
A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage	4
	4
Genomic compatibility and inheritance of hexaploid‐derived Fusarium head blight resistance genes in durum wheat	4
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa	4
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives	4
Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping	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
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	4
Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi	4
Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes	4
Research highlights, The Plant Genome, Volume 15, Issue 1	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
Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study	4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	4
The economics and policy of genome editing in crop improvement	4
Prospects for developing allergen‐depleted food crops	4
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	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
HaploCatcher: An R package for prediction of haplotypes	4
Genomic‐assisted breeding for climate‐smart coffee	4
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes	4
Characterization of evolutionarily distinct rice BAHD‐Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani	3
	3
Deep neural networks for genomic prediction do not estimate marker effects	3
Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses	3
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes	3
Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459	3
A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program	3
Cover Image, Volume 15, Issue 1	3
Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes	3
Double‐digest restriction‐associated DNA sequencing‐based genotyping and its applications in sesame germplasm management	3
High‐resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust	3
Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment	3
Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba	3
Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain	3
Marker‐assisted forward breeding to develop a drought‐, bacterial‐leaf‐blight‐, and blast‐resistant rice cultivar	3
	3
Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection	3
Genomic prediction for the Germplasm Enhancement of Maize project	3
Evolutionary fates of gene‐body methylation and its divergent association with gene expression in pigeonpea	3
Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines	3
Validation of DNA marker‐assisted selection for forage biomass productivity under deficit irrigation in alfalfa	3
Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm	3
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean	3
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	3
Introgression of genes associated with yield enhancement and resistance against bacterial leaf blight and blast diseases into an elite rice variety, Jaya	3
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach	3
DECUSSATEnetwork with flowering genes explains the variable effects ofqDTY12.1to rice yield under drought across genetic backgrounds	3