Fig. 1

The landscape of haplotype-based allelic variation in starch and SGA genes among autotetraploid potato. a, Number of SNPs, InDels and SVs identified in the six tetraploid potato varieties. b, Number of variants containing different counts of alleles. A bi-allelic variation denotes that it only possesses one alternative allele and the reference allele among the six potato cultivars. c, Functional annotation of the identified variants as shown in the pie chart. d, Uneven distribution of allelic variation identified in 38 SGA genes among their haplotypes in the Colomba genome. Number of allelic variations identified in each haplotype is displayed in heat maps. Grey boxes indicate missing data (This gene does not contain this haplotype number). e, Violin plots depict number and distribution of genetic variants in genes carrying different numbers of haplotypes in each of the six potato genomes. The blue dashed lines indicate 75%, median and 25% quartiles. Multiple comparisons are performed using Kruskal-Wallis test with α = 0.001 f, Number of deleterious mutations in genes with one to four haplotypes in the six potato genomes. g, Number of types of haplotypes that can be defined in the six potato cultivars for starch and SGA genes. h, Domestication targeted on a gene encoding a squalene synthase (Soltu.DM.01G050130.3) may lead to a conserved amino acid haplotype structure among tetraploid potato cultivars, which is possibly essential in significant reduction of tuber SGA content in cultivated potato. The number of regulation haplotypes for Soltu.DM.01G050130.3 varies from 2 to 4 across the six potato genomes (left panel), while only one amino-acid haplotype was identified (right panel). A high level of sequence divergence was observed around the predicted transmembrane region of this gene when comparing a wild potato species S. chacoense with cultivated potato. For f and g, data are presented as mean ± SD. One-way ANOVA and Turkey’s multiple comparisons with α = 0.01 are applied