Fig. 1

Co-located loci from the fatty acid genome-wide association analysis and locus selected analysis. a FA composition in 505 rapeseed accessions. Fatty acid phenotypic data (palmitic, stearic, oleic, linoleic, linolenic, eicosanoic, and erucic acids) were collected from seeds of 505 accessions at six sites (Wuhan, Ezhou, Chengdu, Hefei, Kunming, and Lanzhou) over 1 to 4 years. Data for each fatty acid were averaged across multiple years and locations for analysis. b Correlation of phenotypic variation of FA composition. The Pearson correlation coefficient was calculated using multi-year, multi-location BLUP values for FAs in rapeseed. Light blue lines indicate positive correlation, while dark blue lines indicate negative correlation. The thickness of the lines indicates the strength of the correlations between FAs. c Genome-wide association analysis and co-localized QTLs for the composition of six FAs (C16:0, C18:0, C18:1, C18:2, C20:1, and C22:1). d Genome-wide association analysis and co-localized QTLs for seven FA ratios (C18:1/C18:2, C18:1/C18:3, C18:1/C20:1, C18:2/C18:3, C22:1/C18:1, C22:1/C18:2, and C22:1/C18:3). The x-axis represents the rapeseed chromosomes, while the y-axis shows the log₁₀-transformed P values obtained from GWAS. The dotted line marks the significance threshold. By integrating GWAS of different FA compositions and ratios, the co-localized QTLs qFA.A02, qFA.A08, qFA.A09.1, qFA.A09.2, qFA.C02, qFA.C03.1, and qFA.C03.2 were identified. e The log₁₀-transformed P values form C18:1 GWAS plotted against those form seed glucosinolate content (SGC) GWAS. f Signal detection intensity for qFA.A09.1 in GWAS, showing nucleotide diversity (π) with LOWESS smoothed curves. g Manhattan plot showing 2 Mb region upstream and downstream of the qFA.A09.1. Colors indicate the LD (R²) between the lead SNP and each variant in GWAS