Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus

Abstract

Background Regulation 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. Results We 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. Conclusions We 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.

Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

“…However, the asymmetry between subgenomes also opens some interesting questions about their individual contributions to trait regulation. For example, in a recent report, more SNP-eQTLs were identified on the A subgenome compared to the C-subgenome (Tan et al 2022). Our results agree with this finding.…”

Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis

“…Compared with mGWAS, mTWAS tend to use the expression level of a certain gene, eliminating the uncertainty of linkage disequilibrium interval and screening candidate genes more accurately and directly [ 68 , 69 ]. Our previous study comprehensively characterized the transcriptional variability in developing seeds of B. napus and successfully cloned two transcription factors involved in the regulation of SOC from eQTL hotspots87-88 [ 70 ]. The metabolome variation data has brought more information which helped predict novel genes regulating SOC by marker metabolite-based multi-omics analysis.…”

Functional genomics of Brassica napus: Progress, challenges, and perspectives

“…SCARECROW‐LIKE 31 ( BnA09.SCL31 ) and NAC DOMAIN CONTAINING PROTEIN 13 ( BnNAC13s ) were predicted to be the key transcription factors affecting SOC. Overexpression of two homologous copies of BnNAC13s in Arabidopsis was found to significantly alter SOC (Tan et al, 2022a). Further, in combination with metabolomic data, two key genes affecting SOC, TRANSPARENT TESTA 4 ( BnTT4 ) and BnC05.UK were successfully cloned (Li et al, 2023b).…”

“…The large numbers of homologous gene copies lead to gene redundancy and dose effects, making it more difficult to verify gene function. Previous studies have also found imbalances between subgenomes in terms of gene expression, epigenetic activity, and single nucleotide polymorphism variations (Zhou et al, 2017; Zhang et al, 2021; Tan et al, 2022a), which present challenges for deciphering the gene regulatory network in B. napus . Possible reasons for this imbalance include increased heterozygosity between B. napus and B. rapa , as well as limited Cn genomic diversity resulting from primary allopolyploid (Li et al, 2006).…”