ArticleGenome biology2022
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 48 citations in OpenAlex.
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- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- PlantSetDelta: Mining regulatory features to enable interpretable gene set analysis in plants.Plant communications · 2026Article
- Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design.Plant communications · 2026Review
- Allelic variants of IRKI contribute to photosynthetic efficiency by regulating rubisco activase in Populus.Plant physiology · 2025Article
- Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1.Nature communications · 2025Article
- Cell death-inducing DNA fragmentation factor alpha (DFFA)-like effectors (CIDEs) improve lipid droplet (LD) formation and oil accumulation in plant tissues.Plant biotechnology journal · 2025Article
- Integration of BSA-seq and high-resolution mapping reveals genomic regions and candidate genes controlling seed oil accumulation in peanut (Arachis hypogaea L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A panoramic view of cotton resistance toiMeta · 2025Article
- GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize.Plant communications · 2025Article
- A system genetics analysis uncovers the regulatory variants controlling drought response in wheat.Plant biotechnology journal · 2025Article
- Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds.Genome biology · 2025Article
- Genetic and transcriptome analyses of the effect of genotype-by-environment interactions on Brassica napus seed oil content.The Plant cell · 2025Article
- A rare dominant alleleScience advances · 2025Article
- Mining the oil code: New insights behind oil production in Brassica napus.Plant physiology · 2024Article
- Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1.Biotechnology for biofuels and bioproducts · 2023Article
- Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis.Genome biology · 2023Article
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Authors and funding
23 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRegulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an important trait of B. napus.
resultsWe perform a comprehensive analysis of the transcriptional variability in the seeds of B. napus at two developmental stages, 20 and 40 days after flowering (DAF). We detect 53,759 and 53,550 independent expression quantitative trait loci (eQTLs) for 79,605 and 76,713 expressed genes at 20 and 40 DAF, respectively. Among them, the local eQTLs are mapped to the adjacent genes more frequently. The adjacent gene pairs are regulated by local eQTLs with the same open chromatin state and show a stronger mode of expression piggybacking. Inter-subgenomic analysis indicates that there is a feedback regulation for the homoeologous gene pairs to maintain partial expression dosage. We also identify 141 eQTL hotspots and find that hotspot87-88 co-localizes with a QTL for the seed oil content. To further resolve the regulatory network of this eQTL hotspot, we construct the XGBoost model using 856 RNA-seq datasets and the Basenji model using 59 ATAC-seq datasets. Using these two models, we predict the mechanisms affecting the seed oil content regulated by hotspot87-88 and experimentally validate that the transcription factors, NAC13 and SCL31, positively regulate the seed oil content.
conclusionsWe comprehensively characterize the gene regulatory features in the seeds of B. napus and reveal the gene networks regulating the seed oil content of B. napus.
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