Fig. 4

Selection for decrease in heterozygosity associated with domestication of the large starchy storage root (SR) of cassava. a Morphological differences in SR between wild and cultivated cassavas after 350 d of cultivation. b Differences in starch content of SR between wild progenitors and cultivars after 350 d cultivation. c Differences between wild progenitors and cultivars in the expression of genes identified in selection sweeps (above 99% threshold) and related to growth and development in SR at 350 days after planting. Annotation of these genes is shown in Additional file 19: Table S19. d Selection signal detected in MeTIR1 and MeAHL17. The green rectangle indicates the selection signal region. The dashed red and blue lines represent the position (chr2:11,843,579) of a core SNP in the upstream of MeTIR1 and the position (chr2: 11,671,475) of a core SNP in the upstream of MeAHL17, respectively. e Comparison of MeTIR1 expression levels (FPKM) in SR between wild progenitors and cultivars at 350 days after planting. f MeTIR1 gene model. The dashed red line represents the position of the core SNP in the upstream region of MeTIR1. g Frequency of the SNP variants in MeTIR1 in wild and cultivated cassavas. h Box plots of SR starch content based on the SNPs of CC, CG, and GG. The symbol n represents the number of accessions with the same genotype. i Differences in expression of MeTIR1 alleles in SR at 350 d after planting among CC, CG, and GG containing cultivars. j Comparison of MeAHL17 expression levels in SR at 350 days after planting between wild progenitors and cultivars. k MeAHL17 gene model. The dashed red line represents the position of the core SNP in the promoter region of MeAHL17. l Comparison of activities between A-containing and G-containing MeAHL17 promoter regions (300 bp and 600 bp upstream of transcription start site) in dual luciferase assay. Each sample contains 8 biological replicates. m Frequency of the SNP variants in the MeAHL17 gene in wild and cultivated cassavas. n Box plots of SR weight based on the SNPs of AA, AG, and GG. The symbol n represents the number of accessions with the same genotype. o Differences in expression of MeAHL17 in SR at 350 days after planting among AA, AG, and GG containing cultivars. The data in e and j was detected by RNA-Seq and the data in i and o was examined by qRT-PCR. The symbol n represents the number of accessions. Each accession contains three biological replicates. The data for biological replicates were used to draw the box plots. For e, h, i, j, l, n, and o, the center line represents the median, box limits indicate the upper and lower quartiles, and whiskers denote the range of the data. The significance of difference in this figure was derived with two-tailed t-test (*P < 0.05, **P < 0.01)