ArticleScientific reports2016
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 81 citations in OpenAlex.
- Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens.The Plant journal : for cell and molecular biology · 2026Review
- Evolution of the TCP gene family and pan-genome analysis in tea (Camellia sinensis).BMC plant biology · 2026Article
- Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1.Nature communications · 2025Article
- Beyond gene sequences: Pan-transcriptome links transcriptional complexity to functional diversity.Plant communications · 2025Article
- Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.Functional & integrative genomics · 2025Review
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- Evolutionary conservation and enhanced basal immunity of the ZmNBS gene family in maize.Frontiers in plant science · 2025Article
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
- Does one subgenome become dominant in the formation and evolution of a polyploid?Annals of botany · 2023Article
- Mapping of QTLs for morphophysiological and yield traits under water-deficit stress and well-watered conditions in maize.Frontiers in plant science · 2023Article
- Unraveling Plant-Pathogen Interactions in Cereals Using RNA-seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A pan-Zea genome map for enhancing maize improvement.Genome biology · 2022Article
- The value of genotype-specific reference for transcriptome analyses in barley.Life science alliance · 2022Article
- Article
- Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids.Plant physiology · 2022Article
- Article
- Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.The New phytologist · 2022Article
- Plant Genotype to Phenotype Prediction Using Machine Learning.Frontiers in genetics · 2022Review
- Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plantHorticulture research · 2022Article
- Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost.Marine biotechnology (New York, N.Y.) · 2021Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as "genotype" to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
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