Figure 4

Population genetic analysis of the 85 Spinacia species. (a) Comparison of the variant data detected by the 82 resequencing accessions and the three complete chloroplast genomes. ‘Both’ indicates that the SNPs detected by 82 resequencing accessions were present in the SNP dataset from the three chloroplast genomes, whereas ‘Single’ indicates that the SNPs were specifically detected in the 82 resequencing accessions. A neighbor-joining tree of 85 Spinacia accession using the spinach variants’ (b) chloroplast genome and (c) nuclear genome. The individuals with asterisks are used to assembled in the study. (d) Variants in S. oleracea, S. turkestancia, and S. tetrandra. Gray lines indicate reference (S. oleracea) homozygous genotype, while red and black lines represent alternative homozygous and heterozygous genotype, respectively. The samples surrounded with blue dotted lines are the 13 S. oleracea clustered with S. turkestanica in (b). The red arrows mean the three conserved variants between S. oleracea and wild progenitors in Fig. 2c. Tet, S. tetrandra; Tuk, S. turkestanica; Ole, S. oleracea. (e) The percentage of variants (from wild or cultivar) in 29 variants existing in 13 S. oleracea clustered with S. turkestanica in Fig. D. Wild-V indicates the variants from wild species, while Cult-V represents the variants from cultivar species. (f) The inheritance patterns of the 13 S. oleracea.