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References from Plant pan-transcriptomics: Integrating structural genomics, isoform diversity, and systems genetics for next-generation breeding. Local targets link to admitted publications; unresolved targets remain external evidence.
A review on integrating bioinformatics tools in modern plant breeding
10.9734/acri/2024/v24i9894 · 2024 · External reference
Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding
10.1007/s10142-025-01633-x · 2025 · External reference
Crop pangenomes
10.18699/vj21.007 · 2021 · External reference
Plant pangenomes for crop improvement, biodiversity and evolution
10.1038/s41576-024-00691-4 · 2024 · External reference
A pan-grass transcriptome reveals patterns of cellular divergence in crops
10.1038/s41586-023-06053-0 · 2023 · External reference
Beyond gene sequences: pan-transcriptome links transcriptional complexity to functional diversity
10.1016/j.xplc.2025.101486 · 2025 · External reference
Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
10.1038/s41597-020-00581-4 · 2020 · External reference
A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity
10.1038/s41588-024-02069-y · 2025 · External reference
Transcriptome profiling of symptomatic vs. asymptomatic grapevine plants reveals candidate genes for plant improvement against trunk diseases
10.1186/s12870-025-06763-9 · 2025 · External reference
Alternative splicing variation: accessing and exploiting in crop improvement programs
10.3390/ijms242015205 · 2023 · External reference
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
10.1038/s41588-024-01769-9 · 2024 · External reference
Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice
10.1093/plcell/koae181 · 2024 · External reference
A super pan-genomic landscape of rice
10.1038/s41422-022-00685-z · 2022 · External reference
Identification of heat-tolerant genes in non-reference sequences in rice by integrating pan-genome, transcriptomics, and QTLs
10.3390/genes13081353 · 2022 · External reference
The long read transcriptome of rice (Oryza sativa ssp. japonica var. Nipponbare) reveals novel transcripts
10.1186/s12284-022-00577-1 · 2022 · External reference
A system genetics analysis uncovers the regulatory variants controlling drought response in wheat
10.1111/pbi.14605 · 2025 · External reference
Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice
10.1093/plcell/koae039 · 2024 · External reference
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication
10.1186/s12864-018-5357-7 · 2019 · External reference
Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
10.1038/s41598-021-96712-x · 2021 · External reference
BaRTv1. 0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
10.1186/s12864-019-6243-7 · 2019 · External reference
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
10.1038/s41467-024-51252-6 · 2024 · External reference
The value of genotype-specific reference for transcriptome analyses in barley
10.26508/lsa.202101255 · 2022 · External reference
Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus
10.1007/s00122-025-04867-2 · 2025 · External reference
Plant graph-based pangenomics: techniques, applications, and challenges
2025 · External reference
De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
10.1038/s41467-025-64046-1 · 2025 · External reference
Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes
10.3390/biom13091403 · 2023 · External reference
Pan-transcriptomics and its applications
2020 · External reference
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation
10.1038/srep18936 · 2016 · External reference
A large-scale integrated transcriptomic atlas for soybean organ development
10.1016/j.molp.2025.02.003 · 2025 · External reference
A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture
10.1093/g3journal/jkad206 · 2023 · External reference
Molecular and evolutionary processes generating variation in gene expression
10.1038/s41576-020-00304-w · 2021 · External reference
Prokaryote pangenomes are dynamic entities
10.1016/j.mib.2022.01.005 · 2022 · External reference
Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation
10.1105/tpc.114.130773 · 2014 · External reference
Identification of new genomic loci for seed protein and oil content in the soybean pangenome using genome-wide association and haplotype analyses
10.1007/s00122-025-05020-9 · 2025 · External reference
Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton
10.3389/fpls.2022.988647 · 2022 · External reference
Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits
10.1186/s12864-019-6174-3 · 2019 · External reference
Cis–trans controls and regulatory novelty accompanying allopolyploidization
10.1111/nph.15515 · 2019 · External reference
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
10.1186/s13059-023-02909-w · 2023 · External reference
Structural variation in the pangenome of wild and domesticated barley
10.1038/s41586-024-08187-1 · 2024 · External reference
Insights into the maize pan-genome and pan-transcriptome
10.1105/tpc.113.119982 · 2014 · External reference
Unresolved reference
External reference
A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development
10.1186/s12864-025-11360-z · 2025 · External reference
Transcriptome time-course analysis in the whole period of cotton fiber development
2022 · External reference
Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis
10.1093/hr/uhac100 · 2022 · External reference
Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)
10.1016/j.jia.2024.11.026 · 2025 · External reference
Sugarcane pan-transcriptome identifying a master gene ScHCT regulating lignin and sugar traits
10.1021/acs.jafc.4c10101 · 2025 · External reference
A pangenome and pantranscriptome of hexaploid oat
10.1038/s41586-025-09676-7 · 2026 · External reference
Genomic variation within the maize stiff-stalk heterotic germplasm pool
10.1002/tpg2.20114 · 2021 · External reference
Plant pan-genomics: recent advances, new challenges, and roads ahead
10.1016/j.jgg.2022.06.004 · 2022 · External reference
Natural variation in the promoter of GmSPL9d affects branch number in soybean
10.3390/ijms25115991 · 2024 · External reference
Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response
10.3389/fpls.2016.01448 · 2016 · External reference
Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice
10.1016/j.pbi.2017.02.004 · 2017 · External reference
Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions
10.1038/s41588-024-01957-7 · 2024 · External reference
rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue
10.1371/journal.pgen.1010071 · 2022 · External reference
Genome-wide association analyses reveal the importance of alternative splicing in diversifying gene function and regulating phenotypic variation in maize
10.1105/tpc.18.00109 · 2018 · External reference
Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes
10.1186/s12859-022-05023-z · 2022 · External reference
Bypassing miRNA-mediated gene regulation under drought stress: alternative splicing affects CSD1 gene expression
10.1007/s11103-017-0642-4 · 2017 · External reference
Transposable elements in plant genomics: drivers of evolution, adaptation, and crop improvement
10.9734/jabb/2025/v28i42203 · 2025 · External reference
Connecting genome structural variation with complex traits in crop plants
10.1007/s00122-018-3233-0 · 2019 · External reference
Transposable elements in zea: their role in genetic diversity and evolution
2024 · External reference
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
10.1093/nar/gkad578 · 2023 · External reference
Beyond the genome: the role of functional markers in contemporary plant breeding
10.3389/fpls.2025.1637299 · 2025 · External reference
Naught all zeros in sequence count data are the same
10.1016/j.csbj.2020.09.014 · 2020 · External reference
Precisely modeling zero-inflated count phenotype for rare variants
10.1002/gepi.22438 · 2022 · External reference
Widespread impact of transposable elements on the evolution of post-transcriptional regulation in the cotton genus Gossypium
10.1186/s13059-025-03534-5 · 2025 · External reference
Perspective on alternative splicing and proteome complexity in plants
10.1016/j.tplants.2019.02.006 · 2019 · External reference
Alternative splicing dynamics in plant adaptive responses to stress
10.1146/annurev-arplant-083123-090055 · 2025 · External reference
Transcriptional and post-transcriptional regulatory networks controlling cotton fibre development
10.1007/s11103-026-01715-9 · 2026 · External reference
The role of alternative splicing in adaptation and evolution
10.1016/j.tree.2021.11.010 · 2022 · External reference
Alternative splicing: an efficient regulatory approach towards plant developmental plasticity
10.1002/wrna.1758 · 2023 · External reference
Nitric oxide working: no worries about heat stress
10.1016/j.tplants.2023.05.006 · 2023 · External reference
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis
10.1038/s41467-020-16390-7 · 2020 · External reference
Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation
10.1186/s43897-023-00066-z · 2023 · External reference
Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes
10.1007/s00438-009-0506-y · 2010 · External reference
ABA-induced alternative splicing drives transcriptomic reprogramming for drought tolerance in barley
10.1186/s12870-025-06485-y · 2025 · External reference
PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice
10.1111/tpj.14120 · 2019 · External reference
A survey of best practices for RNA-seq data analysis
10.1186/s13059-016-0881-8 · 2016 · External reference
Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows
10.1186/s13007-023-01091-1 · 2023 · External reference
Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease
10.1093/hmg/ddac196 · 2022 · External reference
Hidden genetic regulation of human complex traits via brain isoforms
10.1007/s43657-023-00100-6 · 2023 · External reference
A role for heritable transcriptomic variation in maize adaptation to temperate environments
10.1186/s13059-023-02891-3 · 2023 · External reference
A Genome-Wide Alternative Splicing Analysis of Gossypium arboreum and Gossypium raimondii During Fiber Development
10.3390/plants13192816 · 2024 · External reference
Alternative splicing during fiber development in G. hirsutum
10.3390/ijms241411812 · 2023 · External reference
Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape (Brassica napus l.)
10.1007/s11032-022-01314-8 · 2022 · External reference
Mapping intron retention events contributing to complex traits using splice quantitative trait locus
10.1186/s13007-023-01048-4 · 2023 · External reference
Alternative splicing as a source of phenotypic diversity
10.1038/s41576-022-00514-4 · 2022 · External reference
Introgressions lead to reference bias in wheat RNA-seq analysis
10.1186/s12915-024-01853-w · 2024 · External reference
Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
10.1186/s12864-021-07577-3 · 2021 · External reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
10.1038/s41587-019-0201-4 · 2019 · External reference
Transcriptomics in the era of long-read sequencing
2025 · External reference
LongStitch: high-quality genome assembly correction and scaffolding using long reads
10.1186/s12859-021-04451-7 · 2021 · External reference
White paper: standards for handling and analyzing plant pan-genomes
10.12688/f1000research.166538.1 · 2025 · External reference
Crop Transcriptome Response for Abiotic Stress Tolerance
2025 · External reference
Leveraging single-cell populations to uncover the genetic basis of complex traits
10.1146/annurev-genet-022123-110824 · 2023 · External reference
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
10.1038/s41592-022-01731-9 · 2023 · External reference
Variation graph toolkit improves read mapping by representing genetic variation in the reference
10.1038/nbt.4227 · 2018 · External reference
Identification and Analysis of the AP2/ERF Gene Family in Barley Based on Pan-Genome and Pan-Transcriptome
10.1021/acs.jafc.5c05138 · 2025 · External reference
10.20944/preprints202506.1049.v1
10.20944/preprints202506.1049.v1 · External reference
A pan-Zea genome map for enhancing maize improvement
10.1186/s13059-022-02742-7 · 2022 · External reference
De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome
2024 · External reference
A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study
10.1186/s12864-024-10931-w · 2024 · External reference
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs
10.1002/tpg2.20177 · 2022 · External reference
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification
10.1111/tpj.15871 · 2022 · External reference
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
10.1186/s13059-022-02711-0 · 2022 · External reference
The FAIR Guiding Principles for scientific data management and stewardship
10.1038/sdata.2016.18 · 2016 · External reference
Exploiting plant transcriptomic databases: Resources, tools, and approaches
10.1016/j.xplc.2022.100323 · 2022 · External reference
The role of pangenomics in orphan crop improvement
10.1038/s41467-024-55260-4 · 2025 · External reference
A pan-transcriptome analysis indicates efficient downregulation of the FIB genes plays a critical role in the response of alfalfa to cold stress
10.3390/plants11223148 · 2022 · External reference
Comparative analysis of chloroplast pan-genomes and transcriptomics reveals cold adaptation in Medicago sativa
10.3390/ijms25031776 · 2024 · External reference
A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification
10.1016/j.xplc.2023.100791 · 2024 · External reference
Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus
2024 · External reference
The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content
10.1111/pbi.13600 · 2021 · External reference
Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton
10.1038/s41467-024-55309-4 · 2024 · External reference
LsRTDv1, a reference transcript dataset for accurate transcript-specific expression analysis in lettuce
10.1111/tpj.16978 · 2024 · External reference
AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data
2016 · External reference
High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica
10.3389/fgene.2022.995072 · 2022 · External reference
Transcriptomics in the era of long-read sequencing
10.1038/s41576-025-00828-z · 2025 · External reference
Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data
10.1038/s41467-024-48117-3 · 2024 · External reference
RNA Sequencing Platforms and Bioinformatics Tools
2026 · External reference
Unresolved reference
2017 · External reference
Allele and transcriptome mining in Gossypium hirsutum reveals variation in candidate genes at genetic loci affecting cotton fiber quality and textile flammability
10.1186/s12870-025-06306-2 · 2025 · External reference
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome
10.1093/nar/gks1125 · 2013 · External reference
MaizeGDB: the maize genetics and genomics database
2016 · External reference
WheatCENet: a database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors
10.1016/j.gpb.2022.04.007 · 2023 · External reference
SoyOmics: a deeply integrated database on soybean multi-omics
10.1016/j.molp.2023.03.011 · 2023 · External reference
The evolution of soybean knowledge base (SoyKB)
2016 · External reference
CottonMD: a multi-omics database for cotton biological study
10.1093/nar/gkac863 · 2023 · External reference
PeanutBase and other bioinformatic resources for peanut
2016 · External reference
EORNA, a barley gene and transcript abundance database
10.1038/s41597-021-00872-4 · 2021 · External reference
Nextflow enables reproducible computational workflows
10.1038/nbt.3820 · 2017 · External reference
Snakemake—a scalable bioinformatics workflow engine
10.1093/bioinformatics/bts480 · 2012 · External reference
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
10.1186/s12859-023-05254-8 · 2023 · External reference
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
10.1186/s13059-024-03322-7 · 2024 · External reference
Producing polished prokaryotic pangenomes with the Panaroo pipeline
10.1186/s13059-020-02090-4 · 2020 · External reference
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
10.1093/bioinformatics/btp472 · 2009 · External reference
Cytoscape: a software environment for integrated models of biomolecular interaction networks
10.1101/gr.1239303 · 2003 · External reference
CoExpNetViz: comparative co-expression networks construction and visualization tool
10.3389/fpls.2015.01194 · 2016 · External reference
Evaluation and comparison of computational tools for RNA-seq isoform quantification
10.1186/s12864-017-4002-1 · 2017 · External reference
A comprehensive methodological review of major developments in bioinformatics pipelines for transcriptomic data analysis
2025 · External reference
A pangenome analysis pipeline provides insights into functional gene identification in rice
10.1186/s13059-023-02861-9 · 2023 · External reference
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes
10.1002/tpg2.20221 · 2022 · External reference
PanEffect: a pan-genome visualization tool for variant effects in maize
10.1093/bioinformatics/btae073 · 2024 · External reference
BarleyOmics: A comprehensive multi-omics database of barley
10.1016/j.molp.2025.07.002 · 2025 · External reference
CottonGen: the community database for cotton genomics, genetics, and breeding research
10.3390/plants10122805 · 2021 · External reference
BrassicaEDB: a gene expression database for Brassica crops
10.3390/ijms21165831 · 2020 · External reference
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice
10.1038/s41467-025-62887-4 · 2025 · External reference
Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato
10.1111/tpj.13706 · 2017 · External reference
Integrated Isoform-Resolved Transcriptomic Analysis of Gossypium barbadense and Gossypium hirsutum Fibers
2024 · External reference
Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes
2025 · External reference
Diversity of lncRNAs in the pan-transcriptome of maize inbred lines
10.1186/s12864-025-12242-0 · 2026 · External reference
Pan-transcriptomic profiling demarcates serendipita indica-phosphorus mediated tolerance mechanisms in rice exposed to arsenic toxicity
10.1186/s12284-023-00645-0 · 2023 · External reference
Harnessing Multi-Omics and Predictive Modeling for Climate-Resilient Crop Breeding: From Genomes to Fields
10.3390/genes16070809 · 2025 · External reference
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement
2025 · External reference
An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development
10.1186/s13059-022-02620-2 · 2022 · External reference
Systematical identification of splicing regulatory cis-elements and cognate trans-factors
10.1016/j.ymeth.2013.08.019 · 2014 · External reference
Systems genomics of salinity stress response in rice
10.7554/elife.99352.3 · 2025 · External reference
The exon junction complex undergoes a compositional switch that alters mRNP structure and nonsense-mediated mRNA decay activity
10.1016/j.celrep.2018.11.046 · 2018 · External reference
The genetic regulation of alternative splicing in Populus deltoides
10.3389/fpls.2020.00590 · 2020 · External reference
Complexity of the alternative splicing landscape in plants
10.1105/tpc.113.117523 · 2013 · External reference
Uncovering the impacts of alternative splicing on the proteome with current omics techniques
10.1002/wrna.1707 · 2022 · External reference
Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana
10.3389/fpls.2019.01160 · 2019 · External reference
Advances in alternative splicing identification: deep learning and pantranscriptome
10.3389/fpls.2023.1232466 · 2023 · External reference
Stress-induced changes in alternative splicing landscape in rice: functional significance of splice isoforms in stress tolerance
10.3390/biology10040309 · 2021 · External reference
Methods in genome, pan-genome, pan-transcriptome, and gene regulatory network (GRN) construction and analysis
2023 · External reference
Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis
10.1016/j.febslet.2015.09.023 · 2015 · External reference
Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds
10.3389/fpls.2025.1569565 · 2025 · External reference
Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat
10.1038/s42003-023-04781-7 · 2023 · External reference
Landscape of structural variants reveals insights for local adaptations in the Asian corn borer
10.1016/j.celrep.2024.114928 · 2024 · External reference
Exploring Alternative Splicing in Response to Salinity: A Tissue-Level Comparative Analysis Using Arabidopsis thaliana Public Transcriptomic Data
10.3390/plants14071064 · 2025 · External reference
GWAS and eQTL analyses reveal genetic components influencing the key fiber yield trait lint percentage in upland cotton
10.1111/tpj.70036 · 2025 · External reference
Grapevine adaptation to cold and heat stress
2025 · External reference
Integrative Genomics and Precision Breeding for Stress-Resilient Cotton: Recent Advances and Prospects
10.3390/agronomy15102393 · 2025 · External reference
eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction
10.1186/s12864-022-08690-7 · 2022 · External reference
Comparative transcriptome and metabolome profiling unveil genotype-specific strategies for drought tolerance in cotton
2025 · External reference
Genotype by environment interactions in gene regulation underlie the response to soil drying in the model grass Brachypodium distachyon
10.1093/molbev/msaf218 · 2025 · External reference
Pangenome-wide association study and transcriptome analysis reveal a novel QTL and candidate genes controlling both panicle and leaf blast resistance in rice
10.1186/s12284-024-00707-x · 2024 · External reference
Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat
10.1016/j.xplc.2024.100879 · 2024 · External reference
Regulation of alternative splicing in response to temperature variation in plants
10.1093/jxb/erab232 · 2021 · External reference
Overexpression of the maize Teosinte Branched1 gene in wheat suppresses tiller development
10.1007/s00299-008-0543-8 · 2008 · External reference
Identification of a major QTL and its candidate genes controlling stem strength in soybean via QTL mapping and GWAS
10.1016/j.cj.2025.08.013 · 2025 · External reference
Quality attributes for barley malt:“The backbone of beer
10.1111/1750-3841.15858 · 2021 · External reference
Genetic analysis of grain and malt quality in an elite barley population
10.1007/s11032-016-0554-z · 2016 · External reference
Genetic control and high temperature effects on starch biosynthesis and grain quality in rice
10.3389/fpls.2021.757997 · 2021 · External reference
Resistant starch formation in rice: Genetic regulation and beyond
10.1016/j.xplc.2022.100329 · 2022 · External reference
Nutritional genomic approach for improving grain protein content in wheat
10.3390/foods12071399 · 2023 · External reference
Genome-wide association and RNA-Seq analyses reveal a potential candidate gene related to oil content in soybean seeds
10.3390/ijms25158134 · 2024 · External reference
Genome-wide association and RNA-seq analyses reveal a potential gene related to linolenic acid in soybean seeds
10.7717/peerj.16138 · 2023 · External reference
Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley
10.3390/plants14010028 · 2024 · External reference
Mapping regulatory variants controlling gene expression in drought response and tolerance in maize
10.1186/s13059-020-02069-1 · 2020 · External reference
Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon
10.1111/mec.16661 · 2022 · External reference
From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding
2025 · External reference
Analysis of allelic imbalance in rice hybrids under water stress and association of asymmetrically expressed genes with drought-response QTLs
10.1186/s12284-016-0123-4 · 2016 · External reference
Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for human bone mineral density GWAS associations
10.7554/elife.77285 · 2022 · External reference
Understanding omics driven plant improvement and de novo crop domestication: some examples
10.3389/fgene.2021.637141 · 2021 · External reference
10.1186/s12864-018-5357-7
10.1186/s12864-018-5357-7 · External reference
Trade-offs among resilience, robustness, stability, and performance and how we might study them
10.1093/icb/icab178 · 2021 · External reference
Durum wheat genome highlights past domestication signatures and future improvement targets
10.1038/s41588-019-0381-3 · 2019 · External reference
Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean
10.1105/tpc.114.124040 · 2014 · External reference
10.1007/978-3-030-38281-0
10.1007/978-3-030-38281-0 · 2020 · External reference
The ecology and evolution of pangenomes
10.1016/j.cub.2019.08.012 · 2019 · External reference
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
2013 · External reference
The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication
10.1111/tpj.13181 · 2016 · External reference
Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security
10.1111/nph.18021 · 2022 · External reference
Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome
10.1371/journal.pgen.1004073 · 2014 · External reference
Domestication over speciation in allopolyploid cotton species: A stronger transcriptomic pull
10.3390/genes14061301 · 2023 · External reference
Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
10.1186/s13059-021-02351-w · 2021 · External reference
A pangenome reference of wild and cultivated rice
2025 · External reference
Pan-genome miRNomics in Brachypodium
10.3390/plants10050991 · 2021 · External reference
Utilizing a pan-transcriptome reveals genotype-specific responses to iron deficiency in Sorghum bicolor
2025 · External reference
Pan-transcriptomic analysis of Solanum tuberosum NLR genes regulating resistance to Phytophthora infestans
2021 · External reference
Pan-genome Analysis Reveals Hidden Diversity and Selection Signatures of Auxin Response Factors (ARFs) Associated with Breeding in Barley
2025 · External reference
Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)
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Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways
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Pan-genome analysis reveals the abundant gene presence/absence variations among different varieties of melon and their influence on traits
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Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
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The barley pan-genome reveals the hidden legacy of mutation breeding
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