Plant Genome

Article	Citations
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	187
Wheat's war against stripe rust: Integrating host immunity, genomics and breeding for durable resistance	115
Correction to “Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato”	54
Genetic identification and characterization of novel loci for flag leaf morphology traits in Chinese endemic wheat	51
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	50
Genetic dissection of the root system architecture QTLome and its relationship with early shoot development, breeding and adaptation in durum wheat	49
Genetic control of root architectural traits under drought stress in spring barley ( Hordeum vulgare L.)	47
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	43
Chromosome‐level genome of Zoysia sinica in the intertidal zone reveals genomic insights into waterlogging stress adaptation	40
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem du	40
Genomic and biochemical comparison of allelic triple‐mutant lines derived from conventional breeding and multiplex gene editing	39
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	39
A novel allele of Days to Heading 8 promotes heading, potentially widening indica rice adaptation in Japan	37
A chickpea MAGIC population to dissect the genetics of complex traits	36
Development of user‐selectable diverse sets of cultivated and wild soybean germplasm for genetic and breeding applications	34
Trait mapping differentiates loci influencing spike and flag leaf glaucousness in wheat	34
Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean ( Lablab purpureus	34
Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high‐throughput RNA sequencing	34
TPG 2021 Publisher's Report	34
Transcript profiling of hairy vetch ( Vicia villosa Roth) identified interesting genes for seed dormancy	33
Correction to “Genome‐wide association study identifies QTL and candidate genes for grain size and weight in a Triticum turgidum collection”	31
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	31
Genome‐wide association study of carotenoids in maize kernel	28
Targets and strategies to design soybean seed composition traits	28
Alfalfa genomic selection for different stress‐prone growing regions	26

Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	26
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium<	26
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	25
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	24
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	24
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	23
Integrative chromosome‐scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma	23
Thanks to Our Reviewers, The Plant Genome , 2021	23
Genome‐wide association studies reveal genetic control of nutritional quality, milling traits, and agronomic characteristics in oat ( Avena sativa L.)	23
	23
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora	22
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	22
Variant filters using segregation information improve mapping of nectar‐production genes in sunflower ( Helianthus annuus L.)	21
Decoding the CBL gene family in durum wheat: Insights into dual ABA signaling pathways and calcium‐mediated drought tolerance	21
Editorial Board	20
	20
Optimizing genomic prediction with transfer learning under a ridge regression framework	20
	20
Genome‐wide association study of seed mineral nutrients in peas ( Pisum sativum L.)	20
The Plant Genome special section: Modern improvement of tropical crops	20
Natural variation and underlying genetic loci of γ‐oryzanol in Asian cultivated rice seeds	19
Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes	19
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	19
Mutations in the dwarf3 gene confer height stability in sorghum	19
Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm	19
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	19
Integration of physiological and remote sensing traits for improved genomic prediction of wheat yield	19
Diverse reference genomes detect variants in the US winter wheat	18
Identification of resistance sources and genomic regions regulating spot blotch resistance in Asian bread wheat ( Triticum aestivum L.) via genome‐wide a	18
The genome of a low‐seeded mandarin, Premier, displays major structural changes due to gamma irradiation	17
Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame	17
Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits	17
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	17
	17
Salinity stress tolerance prediction for biomass‐related traits in maize ( Zea mays L.) using genome‐wide markers	17
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	17
The mirage of DNA methylation in transcriptional regulation of plants	17
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	17
Analysis of candidate genes identified via genome‐wide association analysis of sugar‐related traits in maize kernels	16
Genetic control of grain amino acid composition in a UK soft wheat mapping population	16
A chromosome‐level genome of mango exclusively from long‐read sequence data	16
The conservation of gene models can support genome annotation	16
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum	16
Common signatures of selection reveal target loci for breeding across soybean populations	15
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	15
Multi‐trait/environment sparse genomic prediction using the SFSI R‐package	15
Cover Image, Volume 15, Issue 2	15
IGTCM: An integrative genome database of traditional Chinese medicine plants	15
Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2	15
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	15

Integrated chloroplast genomics and whole‐genome resequencing reveals demographic history and selection signatures of black walnuts	14
Erratum to: Fertilization of grapevine based on gene expression	14
MicroRNAs‐mediated heat stress regulations in plants: Mechanisms and targets	14
Do maize chromosomes contribute to genetic variance in proportion to their size in elite populations?	14
Erratum to “Alanine aminotransferase contributes to hypoxia sensitivity and dormancy in barley seeds”	14
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat ( Triticum aestivum L.)	14
Fine mapping and functional analysis of the candidate gene OFP17 , regulating both seed and fruit sizes in cotton	14
The Plant Genome Annual Report, 2024	14
Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy	14
Editorial Board	14
Genetic mapping of a chickpea ( Cicer arietinum L.) diversity panel for mineral biofortification towards human nutrition	13
Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean	13
Pangenome insights into structural variation and functional diversification of barley CCT motif genes	13
Research Highlights, The Plant Genome , Volume 15, Issue 4	13
An extensible vector toolkit and parts library for advanced engineering of plant genomes	13
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change	13
Correction to “Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback”	13
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	13
Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phy	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
Issue Information	13
Chromosome‐level genome assembly of Indian mangrove ( Ceriops tagal ) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat ( Triticum aestivum	13
Genome‐wide association studies and genomics‐informed breeding for tuber dormancy in tetraploid potatoes	13
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	12
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	12
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	12
Development of functional markers and expression analysis for a Peroxidase gene TaPod‐A3 on chromosome 7AL in wheat	12
Genetic control of wheat flour end‐use quality and rheology by genome‐wide association studies	12
Diversity of cereal rye ( Secale cereale ) germplasm in the Southeast United States	12
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	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
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	12
Seed protein electrophoresis in plant genetics: Commemorating the pioneering contributions of Prof. Chittaranjan Kole and team to the foundation of plant proteomics	12
k ‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	12
Dissecting multi‐rust resistance in wheat through genome‐wide association study, haplotype analysis, and marker validation	11
Harnessing genomic resources for passion fruit improvement: Progress and prospects	11
First whole genome sequence of a diploid crop wild relative of the Andean tuber “oca”: Annotation and comparative genomic analysis of  Oxalis oulophora	11
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	11
Unveiling the genetic determinants of germination efficiency in common bermudagrass: A genome‐wide association study	11
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	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 study and KASP marker development for starch quality traits in wheat	10
Identification and genomic location of resistance to bacterial leaf streak of barley	10
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2	10
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	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
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	10
Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study	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	9
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	9
Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses	9
Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat	9
A chromosome‐scale genome of Sarracenia purpurea reveals a significant expansion of plant defense and stress response gene families following paleopolypl	9
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	9
Genomic selection: Essence, applications, and prospects	9
	9
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	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
Current technical advancements in plant epitranscriptomic studies	9
Genomic prediction in Persian walnut: Optimization levers according to genetic architecture of complex traits	9
Seed shattering in a North American Oryzeae grain: Developmental and genomic signatures of early domestication	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
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	9
Genomic selection of soybean ( Glycine max ) for genetic improvement of yield and seed composition in a breeding context	9
Distinct classes of 21‐ and 24‐nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development	8
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	8
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	8
A benchmarking of genomic selection models for predicting grain‐yield related traits using haplotype‐based and genome‐wide association study‐based markers in rice	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
Identification and mapping of quantitative trait loci for Fusarium head blight resistance in a synthetic hexaploid × hard red spring wheat population	8
Research highlights, The Plant Genome , Volume 16, Issue 4	8

Genome‐wide exploration of bacterial leaf blight resistance and fine mapping of major resistance gene ( Bb13 ) in upland cotton (	8
Genomic prediction of tocochromanols in exotic‐derived maize	8
Genome‐wide identification and biological relevance of broccoli aquaporins	8
Genetic components associated with R2 and R4 powdery mildew resistance in hop	8
Validation of sorghum quality control (QC) markers across African breeding lines	8
ConvCGP: A convolutional neural network to predict genetic values of agronomic traits from compressed genome‐wide polymorphisms	8
The PIN2 ortholog in barley modifies root gravitropism and architecture	8
Editorial Board	8
Leaf transcriptome differences between diploid and tetraploid bahiagrass	8
Enhancing prediction accuracy of key biomass partitioning traits in wheat using multi‐kernel genomic prediction models integrating secondary traits and environmental covariates	8
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	8
Genetic variation in a tepary bean ( Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	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
Environment ensemble models for genomic prediction in common bean ( Phaseolus vulgaris L.)	8
Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato	8
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
k ‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Haplotyping interspecific hybrids by dual alignment to both parental genomes	7
Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize	7
Enhancing crop resilience through elite pre‐breeding lines with key traits for dry direct‐seeded rice	7
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	7
Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement	7
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 low‐coverage skim‐sequencing and imputation pipeline for genomic selection	7
A view of the pan‐genome of domesticated Cowpea ( Vigna unguiculata [L.] Walp.)	7
Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication	7
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	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
Haplotype‐based insights into seminal root angle in barley	6
Erratum to “Identification, characterization, and expression of  Oryza sativa  tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolis	6
Genomic prediction of seed nutritional traits in biparental families of oat ( Avena sativa )	6
Ubiquitin‐like SUMO protease expansion in rice ( Oryza sativa L.)	6
Genomic and phenomic prediction for soybean seed yield, protein, and oil	6
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	6
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	6
RPAD locus controls prostrate growth habit in Oryza nivara	6
Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato ( Solanum tuberosum )	6
Tools and targets: The dual role of plant viruses in CRISPR–Cas genome editing	6
	6
Crop growth model‐enabled genetic mapping of biomass accumulation dynamics in photoperiod‐sensitive sorghum	6
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	6
The Big BIT maize experiment: A large multi‐location, multi‐year, multi‐tester, multi‐population predictive breeding validation study	6
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	5
Editorial Board	5
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	5
Harnessing genomic prediction in Brassica napus through a nested association mapping population	5
Developing drought‐smart, ready‐to‐grow future crops	5
Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids	5
New genomic resources to boost research in reproductive biology to enable cost‐effective hybrid seed production	5
Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
	5
Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava	5
Editorial Board	5
Thanks to Reviewers, The Plant Genome , 2023	5
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	5
Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole‐genome resequence and multi‐environmental data	5
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	5
Hybrid kernels integrating genomic and multispectral data improve wheat genomic prediction accuracy	5
Genome‐wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi	5
Phenotypic plasticity in maize grain yield: Genetic and environmental insights of response to environmental gradients	5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	5
Candidate selective sweeps in US wheat populations	5
Editorial Board	5
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	5
Editorial Board	5
Maize and heat stress: Physiological, genetic, and molecular insights	5
The role of microRNAs in responses to drought and heat stress in peanut ( Arachis hypogaea )	5
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	5
Effectiveness of low‐density high‐throughput marker platform and easy‐to‐measure traits for genomic prediction of biomass yield in oat ( Avena sativa L.)	5
Use of continuous genotypes for genomic prediction in sugarcane	5
The economics and policy of genome editing in crop improvement	4
Genomic prediction for potato ( Solanum tuberosum ) quality traits improved through image analysis	4
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
	4
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes	4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	4
Prospects for developing allergen‐depleted food crops	4
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	4
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	4
Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry	4
The effect of haplotype size on genomic selection accuracy and epistasis: An empirical study in rice	4
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean	4
HaploCatcher: An R package for prediction of haplotypes	4
Genome‐wide association study and molecular marker development for resistance to soybean cyst nematode in soybean	4
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research	4
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	4
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	4
CRISPR‐induced knockouts reveal a dual role for the soybean NFR5α gene in symbiotic nitrogen fixation and root hair development	4
Exploring the efficacy of phenomic and genomic selection for yield and fruit quality traits in strawberry	4
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize	4
Development and characterization of near‐isogenic lines for quantitative trait locus qDT.3B.1 underlying drought tolerance in wheat	4