Population information:
1614 B. juncea accessions have been collected, including 1,387 from Asia, 84 from Europe, 32 from North America, 1 from South America, 11 from Oceania, 3 from Africa, and 96 from unknown regions. Detailed information about the dataset is shown on the table below. Population structure:
Based on the genotypes and origins, 1614 B. juncea accessions can be classified into 10 subpopulations, which are named as O1, O2, O3, O4, O5, O6, U1, V1, V2, V3. The description of these subpopulations can be found in the below table. Regarding the domestication history of these subpopulations, we referred to the study published by Kang et al (Kang et al., 2021). According to their findings, Brassica juncea likely originated in Asia around 8,000-14,000 years ago. The differentiation into the O1 subpopulation occurred around 1,800-4,600 years ago, while the divergence into the O2 subpopulation took place approximately 600-1,300 years ago. The emergence of the O3 subpopulation is estimated to have occurred around 1,200-2,500 years ago, while the V1 subpopulation diverged around 2,500-5,120 years ago. Lastly, the divergence into the V2/V3 subpopulations is estimated to have occurred approximately 600-1,300 years ago.

Supopulation name in BjuIR	Subpopulation name in Kang et al's study	Number	Divergence time (years ago)	Description
O1	G2, G3	256	1800-4600	Seed mustard Mainly come from Central and Western Asia, Northwest China
O2	G4	62	600-1300	Seed mustard mainly come from Southwest China
O3	G6	80	1200-2500	Seed mustard mainly come from South Asia
O4	--	178	--	Seed mustard mainly come from Northwestern India
O5	--	61	--	Seed mustard mainly come from Europe, North America
O6	--	143	--	Seed mustard mainly come from India
U1	--	427	--	Indian mustard with unknown usage
V1	G1	43	2500-5120	Root mustard mainly come from Northeast China and South China
V2	G5	227	600-1300	Leaf mustard mainly come from South China, Japan; Vegetable-use
V3	G5	137	600-1300	Stem mustard come from South China; Vegetable-use

Selective signals:
In order to identify the candidate regions under the selection pressure, nucleotide diversity (π) and Tajima's D, population fixation statistics (F_ST), Cross-population Extended Haplotype Homozygosity (XP-EHH) have been calculated. π was calculated for each subpopulation using VCFtools (v.0.1.16) (Danecek et al., 2011) in a 500-kb sliding window with a step size of 50 kb. Tajima's D was calculated for each subpopulation using VCFtools (v.0.1.16) (Danecek et al., 2011) in a 50 kb sliding window. F_ST, which indicates genomic differentiation between populations, was calculated for each pair of subpopulations using VCFtools (v.0.1.16) in the same window size as that of π. XP-EHH, a haplotype-based method to identify putative regions of recent or ongoing positive selection in genomes, was calculated for each pair of subpopulations by selscan (v.1.2.0) (Szpiech and Hernandez, 2014).

References
1. Akhatar, J., Goyal, A., Kaur, N., Atri, C., Mittal, M., Singh, M.P., Kaur, R., Rialch, I. and Banga, S.S. (2021). Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss. Sci. Rep. 11: 4278.
2. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T. et al. (2011). The variant call format and VCFtools. Bioinformatics 27: 2156-2158.
3. 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.
4. Kang, L., Qian, L., Zheng, M., Chen, L., Chen, H., Yang, L., You, L., Yang, B., Yan, M., Gu, Y. et al. (2021). Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat. Genet. 53: 1392-1402.
5. Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y. et al. (2016). The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat. Genet. 48: 1225-1232.
6. 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.
7. Szpiech, Z.A. and Hernandez, R.D. (2014). selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol 31: 2824-2827.