Extended Data Fig. 5: Genome-wide selective sweep scan and GWAS for seed weight in Brassica juncea.

a, Genome-wide distribution of selective-sweep signals identified through comparisons between G5 or G6 with G2 using XP-CLR values (sliding window = 10 kb, step = 1 kb). The thousand seed weight candidate genes in the selection regions are labeled. b and e, Local Manhattan plot showing the 0.60 - 0.65 Mb and 41.48 - 41.50 Mb region on chromosomes A04 and B05, respectively. The green plots represent the position of these SNPs in CYP78A9 (BjuA04g00760S) and CaM7 (BjuB05g28000S). Three and one SNPs in CYP78A9 and CaM7 are significantly associated with thousand seed weight, respectively. The heatmaps span the SNP markers that show linkage disequilibrium (LD) with the most strongly associated SNPs. The grey dashed lines indicate the significance threshold (-log₁₀^p = 5.0). c and f, Comparison of conserved SNPs specific to six groups in CYP78A9 and CaM7 gene region, respectively. Two haplotypes with frequency greater than 0.01 were identified in CYP78A9 and CaM7 gene region, respectively. d and g, Comparison in thousand seed weight between accessions of three haplotypes in CYP78A9 and CaM7 gene region, respectively. Box edges represent the 0.25 quantile and 0.75 quantile with the median values shown by bold lines. Whiskers extend to data no more than 1.5 times the interquartile range, and remaining data are indicated by dots. p-value was calculated with two-sided t-test.