Plant Genome

Article	Citations
Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola	189
Genetic dissection of the root system architecture QTLome and its relationship with early shoot development, breeding and adaptation in durum wheat	122
Correction to “Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato”	55
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem du	54
Genetic identification and characterization of novel loci for flag leaf morphology traits in Chinese endemic wheat	50
Wheat's war against stripe rust: Integrating host immunity, genomics and breeding for durable resistance	48
Genetic control of root architectural traits under drought stress in spring barley ( Hordeum vulgare L.)	45
Transcriptome analysis of iron over‐accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling	44
Genetic dissection of plant architecture, development, and seed morphology in exotic × elite Upland cotton populations	41
Genome‐wide association studies reveal environment‐dependent genetic associations for plant architecture in regional soybean germplasm	41
Genome‐wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress	41
Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador	39
Genomic and biochemical comparison of allelic triple‐mutant lines derived from conventional breeding and multiplex gene editing	37
Chromosome‐level genome of Zoysia sinica in the intertidal zone reveals genomic insights into waterlogging stress adaptation	37
Genome‐wide association study of carotenoids in maize kernel	36
A novel allele of Days to Heading 8 promotes heading, potentially widening indica rice adaptation in Japan	36
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant	34
A 24‐nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis	34
Alfalfa genomic selection for different stress‐prone growing regions	33
Trait mapping differentiates loci influencing spike and flag leaf glaucousness in wheat	33
Genome‐wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance	31
Correction to “Genome‐wide analysis of theAP2/ERF gene family in Rheum officinale Baill.: Evolution and expression profiling during plant development, ab	30
Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high‐throughput RNA sequencing	29
A chickpea MAGIC population to dissect the genetics of complex traits	28
Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean ( Lablab purpureus	27

Transcript profiling of hairy vetch ( Vicia villosa Roth) identified interesting genes for seed dormancy	26
Development of user‐selectable diverse sets of cultivated and wild soybean germplasm for genetic and breeding applications	26
Correction to “Genome‐wide association study identifies QTL and candidate genes for grain size and weight in a Triticum turgidum collection”	25
A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium<	25
Targets and strategies to design soybean seed composition traits	24
Time‐series multispectral imaging in soybean for improving biomass and genomic prediction accuracy	24
Variant filters using segregation information improve mapping of nectar‐production genes in sunflower ( Helianthus annuus L.)	23
Integrative chromosome‐scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma	23
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Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora	22
Decoding the CBL gene family in durum wheat: Insights into dual ABA signaling pathways and calcium‐mediated drought tolerance	22
Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean	21
Genome‐wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation	21
Genome‐wide association studies reveal genetic control of nutritional quality, milling traits, and agronomic characteristics in oat ( Avena sativa L.)	21
Pan‐NLRome analysis uncovers genetic diversity and evolutionary dynamics among rice, maize and sorghum	21
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing	21
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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
Editorial Board	19
Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes	19
Optimizing genomic prediction with transfer learning under a ridge regression framework	19
Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm	19
Identification of resistance sources and genomic regions regulating spot blotch resistance in Asian bread wheat ( Triticum aestivum L.) via genome‐wide a	18
Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications	18
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding	18
Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks	18
Diverse reference genomes detect variants in the US winter wheat	18
Integration of physiological and remote sensing traits for improved genomic prediction of wheat yield	18
Genome‐wide association study of seed mineral nutrients in peas ( Pisum sativum L.)	17
Genetic control of grain amino acid composition in a UK soft wheat mapping population	17
Salinity stress tolerance prediction for biomass‐related traits in maize ( Zea mays L.) using genome‐wide markers	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
Mutations in the dwarf3 gene confer height stability in sorghum	17
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum	17
Analysis of candidate genes identified via genome‐wide association analysis of sugar‐related traits in maize kernels	16
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The genome of a low‐seeded mandarin, Premier, displays major structural changes due to gamma irradiation	16
Genes and genetic mechanisms contributing to fall armyworm resistance in maize	16
The mirage of DNA methylation in transcriptional regulation of plants	16
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea	15
Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2	15
A chromosome‐level genome of mango exclusively from long‐read sequence data	15
Cover Image, Volume 15, Issue 2	15
Multi‐trait/environment sparse genomic prediction using the SFSI R‐package	15
Genome‐wide analysis of the AP2/ERF gene family in Rheum officinale Baill.: Evolution and expression profiling during plant development, abiotic stresses	15
The conservation of gene models can support genome annotation	15
Editorial Board	14

The Plant Genome Annual Report, 2024	14
IGTCM: An integrative genome database of traditional Chinese medicine plants	14
MicroRNAs‐mediated heat stress regulations in plants: Mechanisms and targets	14
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
Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum	14
Erratum to “Alanine aminotransferase contributes to hypoxia sensitivity and dormancy in barley seeds”	14
Q&A: Methods for estimating genetic gain in sub‐Saharan Africa and achieving improved gains	14
Common signatures of selection reveal target loci for breeding across soybean populations	14
An extensible vector toolkit and parts library for advanced engineering of plant genomes	13
Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean	13
Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy	13
Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools	13
Research Highlights, The Plant Genome , Volume 15, Issue 4	13
Pangenome insights into structural variation and functional diversification of barley CCT motif genes	13
Correction to “Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback”	13
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat ( Triticum aestivum L.)	13
Genome‐wide association studies and genomics‐informed breeding for tuber dormancy in tetraploid potatoes	13
Genome‐wide association of dry (Tamar) date palm fruit color	13
Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phy	13
Issue Information	13
Do maize chromosomes contribute to genetic variance in proportion to their size in elite populations?	13
Genomic‐wide analysis reveals seven in absentia genes regulating grain development in wheat ( Triticum aestivum	13
Fine mapping and functional analysis of the candidate gene OFP17 , regulating both seed and fruit sizes in cotton	13
Genomic and phenotypic characterization of finger millet indicates a complex diversification history	13
Diversity of cereal rye ( Secale cereale ) germplasm in the Southeast United States	12
Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana	12
Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant	12
Genetic mapping of a chickpea ( Cicer arietinum L.) diversity panel for mineral biofortification towards human nutrition	12
Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program	12
Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias	12
Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111	12
Genetic control of wheat flour end‐use quality and rheology by genome‐wide association studies	12
Unveiling the genetic determinants of germination efficiency in common bermudagrass: A genome‐wide association study	11
Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses	11
Seed protein electrophoresis in plant genetics: Commemorating the pioneering contributions of Prof. Chittaranjan Kole and team to the foundation of plant proteomics	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
Development of functional markers and expression analysis for a Peroxidase gene TaPod‐A3 on chromosome 7AL in wheat	11
Comparing artificial‐intelligence techniques with state‐of‐the‐art parametric prediction models for predicting soybean traits	11
Harnessing genomic resources for passion fruit improvement: Progress and prospects	11
Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa	10
Dissecting multi‐rust resistance in wheat through genome‐wide association study, haplotype analysis, and marker validation	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
Genomic selection of soybean ( Glycine max ) for genetic improvement of yield and seed composition in a breeding context	10
Insights into the roles of long noncoding RNAs in the communication between plants and the environment	10
Genome‐wide association studies of a pea germplasm reveal novel markers and candidate genes implicated in resistance to Fusarium oxysporum f. sp.	10
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley	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
Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat	10
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut	10
Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean	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
k ‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel	10
Multi‐trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea	10
Genome‐wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits	10
Genome‐wide association study and KASP marker development for starch quality traits in wheat	10
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Current technical advancements in plant epitranscriptomic studies	9
A chromosome‐scale genome of Sarracenia purpurea reveals a significant expansion of plant defense and stress response gene families following paleopolypl	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
Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data	9
Seed shattering in a North American Oryzeae grain: Developmental and genomic signatures of early domestication	9
Unravelling marker trait associations linking nutritional value with pigmentation in rice seed	9
Multi‐trait genomic selection improves the prediction accuracy of end‐use quality traits in hard winter wheat	9
Optimization of high‐throughput marker systems for genomic prediction in alfalfa family bulks	9
A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger	9
Genetic variation in a tepary bean ( Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance	9
Genomic selection: Essence, applications, and prospects	9
Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut	9
Genetic components associated with R2 and R4 powdery mildew resistance in hop	9
AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning	9
Meta‐QTL analysis and in‐silico transcriptome assessment for controlling chlorophyll traits in common wheat	9
Identification and genomic location of resistance to bacterial leaf streak of barley	9
Genome‐wide identification and biological relevance of broccoli aquaporins	9
Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis	8
Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize	8

Validation of sorghum quality control (QC) markers across African breeding lines	8
Distinct classes of 21‐ and 24‐nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development	8
Editorial Board	8
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR	8
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean	8
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset	8
Leaf transcriptome differences between diploid and tetraploid bahiagrass	8
Research highlights, The Plant Genome , Volume 16, Issue 4	8
The PIN2 ortholog in barley modifies root gravitropism and architecture	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
Enhancing prediction accuracy of key biomass partitioning traits in wheat using multi‐kernel genomic prediction models integrating secondary traits and environmental covariates	8
Genomic prediction of tocochromanols in exotic‐derived maize	8
Genome‐wide exploration of bacterial leaf blight resistance and fine mapping of major resistance gene ( Bb13 ) in upland cotton (	8
Identification and mapping of quantitative trait loci for Fusarium head blight resistance in a synthetic hexaploid × hard red spring wheat population	8
Diversity of fatty acid biosynthesis genes across the soybean pangenome	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
Genome‐wide association study reveals the genetic architecture of drought tolerance in maize using yield‐based resistance indices and transcriptomic evidence	7
ConvCGP: A convolutional neural network to predict genetic values of agronomic traits from compressed genome‐wide polymorphisms	7
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity	7
Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication	7
Machine learning‐driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao	7
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions	7
Genetic diversity and population structure of jute mallow ( Corchorus olitorius L.) global collection to guide conservation and breeding	7
Environment ensemble models for genomic prediction in common bean ( Phaseolus vulgaris L.)	7
Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement	7
Genome‐wide investigation of multiplexed CRISPR‐Cas12a‐mediated editing in rice	7
Haplotyping interspecific hybrids by dual alignment to both parental genomes	7
k ‐mer‐based GWAS enhances the discovery of causal variants and candidate genes in soybean	7
Genome‐wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato	7
Enhancing crop resilience through elite pre‐breeding lines with key traits for dry direct‐seeded rice	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
Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops	6
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Erratum to “Identification, characterization, and expression of  Oryza sativa  tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolis	6
Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative	6
A view of the pan‐genome of domesticated Cowpea ( Vigna unguiculata [L.] Walp.)	6
Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis	6
Crop growth model‐enabled genetic mapping of biomass accumulation dynamics in photoperiod‐sensitive sorghum	6
Genomic prediction of seed nutritional traits in biparental families of oat ( Avena sativa )	6
A low‐coverage skim‐sequencing and imputation pipeline for genomic selection	6
Genomic and phenomic prediction for soybean seed yield, protein, and oil	6
The Big BIT maize experiment: A large multi‐location, multi‐year, multi‐tester, multi‐population predictive breeding validation study	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
Haplotype‐based insights into seminal root angle in barley	6
Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole‐genome resequence and multi‐environmental data	5
Ubiquitin‐like SUMO protease expansion in rice ( Oryza sativa L.)	5
RPAD locus controls prostrate growth habit in Oryza nivara	5
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed	5
Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass	5
Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns	5
Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits	5
Sparse testing designs for optimizing resource allocation in multi‐environment cassava breeding trials	5
Maize and heat stress: Physiological, genetic, and molecular insights	5
Thanks to Reviewers, The Plant Genome , 2023	5
Editorial Board	5
Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain	5
Editorial Board	5
Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci	5
SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection	5
Use of continuous genotypes for genomic prediction in sugarcane	5
The role of microRNAs in responses to drought and heat stress in peanut ( Arachis hypogaea )	5
Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis	5
Genomic selection of maize test‐cross hybrids leveraged by marker sampling	5
Developing drought‐smart, ready‐to‐grow future crops	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
Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress	5
Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes	5
Harnessing genomic prediction in Brassica napus through a nested association mapping population	5
Candidate selective sweeps in US wheat populations	5
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement	5
Hybrid kernels integrating genomic and multispectral data improve wheat genomic prediction accuracy	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
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Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon	5
Editorial Board	5
Prospects for developing allergen‐depleted food crops	4
The economics and policy of genome editing in crop improvement	4
Genetic mapping and haplotype analysis identify novel candidate genes for high night temperature tolerance in winter wheat	4
Exploring the efficacy of phenomic and genomic selection for yield and fruit quality traits in strawberry	4
The effect of haplotype size on genomic selection accuracy and epistasis: An empirical study in rice	4
Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments	4
Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population	4
HaploCatcher: An R package for prediction of haplotypes	4
Integrated GWAS and Fst analysis identify flowering‐time regulatory genes in maize	4
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Genome‐wide association study and molecular marker development for resistance to soybean cyst nematode in soybean	4
Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat	4
Development and characterization of near‐isogenic lines for quantitative trait locus qDT.3B.1 underlying drought tolerance in wheat	4
A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives	4
Understanding the genetic basis of heat stress tolerance in wheat ( Triticum aestivum L.) through genome‐wide association studies	4
Genetic erosion within the Fabada dry bean market class revealed by high‐throughput genotyping	4
CRISPR‐induced knockouts reveal a dual role for the soybean NFR5α gene in symbiotic nitrogen fixation and root hair development	4
Genome‐wide identification of R2R3‐MYB family genes and gene response to stress in ginger	4