In multi-omics analysis, gene expression and population variation data were using T84-66.V2.0 (Yang et al., 2021) as the reference genomes. Genome-wide association study (GWAS), expression quantitative trait loci (eQTL) mapping, and transcriptome-wide association study (TWAS), colocalization analysis (COLOC) and summary data–based Mendelian randomization analysis (SMR) were performed to identify candidate genes and genetic variants associated with phenotypes based on population-level multi-omics data. The GWAS analysis of 16 phenotypes (Harper et al., 2020) identified a total of 129 trait-related genetic loci (P < 6.54e-6). Using GWAS analysis, we identified a total of 129 genetic loci associated with 16 phenotypes (P < 6.54e-6). The eQTL analysis of 204 accessions (Harper et al., 2020) identified 167,343 eQTLs significantly associated with the expression levels of 41,517 genes (P < 6.54e-6). A total of 72 genes significantly associated with eight phenotypes were identified by TWAS (P < 1.74e-5). To identify the candidate genes more precisely, we performed colocalization analysis and SMR analysis by integrating the GWAS signals and eQTL mapping results.

References
1. Harper, A.L., He, Z., Langer, S., Havlickova, L., Wang, L., Fellgett, A., Gupta, V., Kumar Pradhan, A. and Bancroft, I. (2020). Validation of an associative transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits. Plant J. 103: 1885-1893.
2. Yang, J., Wang, J., Li, Z., Li, X., He, Z., Zhang, L., Sha, T., Lyu, X., Chen, S., Gu, Y. et al. (2021). Genomic signatures of vegetable and oilseed allopolyploid Brassica juncea and genetic loci controlling the accumulation of glucosinolates. Plant Biotechnol. J. 19: 2619-2628.