Genetic and transcriptome analyses of the effect of genotype-by-environment interactions on Brassica napus seed oil content

The molecular basis underlying crop traits is complex, with gene-by-environment interactions (GEIs) affecting phenotypes. However, quantitative trait nucleotide (QTN)-by-environment interactions (QEIs) and GEIs for seed oil content (SOC) in oil crops are rare. Here, we detected 11 environmentally specific and 10 stable additive QTNs and 11 QEIs for SOC in rapeseed (Brassica napus) using genome-wide association studies. Weighted gene co-expression network analysis identified 8 Environmental-Developmental Gene co-expression Modules for which the eigengenes correlated with SOC and the environment explained a large proportion of the variance in gene expression. By incorporating information from the multi-omics dataset, 17 candidate genes and 11 candidate GEIs for SOC were predicted. We mined 1 GEI candidate, LIGHT-DEPENDENT SHORT HYPOCOTYLS5 (LSH5), around the environmentally specific QTN qspOC.A02.1 and QEI qeOC.A02.1 detected by climatic indices as covariates. BnaA02.LSH5 was highly expressed in early seed development, and its expression varied significantly across planting sites, with a trend opposite to light-related climatic indices. The BnaA02.lsh5 and BnaC02.lsh5 double mutants had lower SOC, hypocotyl length, photosynthesis, and carbon- and energy-related metabolites compared with wild type. Moreover, BnaA02.LSH5 transcriptionally directly repressed BnaA02.pMDH2 in fatty acid β-oxidation and photosynthetic electron transport. We propose that BnaLSH5 affects seed oil accumulation in response to light intensity. This study provides a basis for creating high-oil germplasm that is adapted to specific environments.