Fig. 2

Soybean chloroplast haplotypes and their distribution. A Chloroplast haplotypes and tag SNPs. The polymorphic sites are shown below the heat map. The name of each site indicates the position (bp) in the reference chloroplast genome. B The overall distribution of chloroplast haplotypes in Glycine max and Glycine soja. The number in parentheses indicates the number of varieties with the respective haplotype. C Network of chloroplast haplotypes in G. max and G. soja. The number of soybean accessions with each haplotype is indicated by the size of the pie chart. D The distributions of soybean chloroplast haplotypes in different countries. E The distributions of soybean chloroplast haplotypes in the main production regions of China. CT1–CT44, Chloroplast haplotypes; CTG1–CTG4, Chloroplast haplotype groups; REF, reference alleles; ALT, alternative alleles; CHL, Chloroplast; HS, Huang-Huai-Hai region and South China; NE, Northeast China; N Korea, North Korea; S Korea, South Korea