Genome sequencing of adapted diploid potato clones

Abstract

Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.

Keywords: StCDF1; breeding; deleterious alleles; diploid potato; genome sequencing; potato.

FIGURE 1

Distribution of SNPs in each genome in the intergenic, intron, and exon regions when compared against (A) DMv6.1 and (B) RHv3.

FIGURE 2

Distribution of CNVs in each genome when compared against (A) DMv6.1 and (B) RHv3.

FIGURE 3

Phylogenetic tree of the nine diploid clones based on the SNP analysis using the DMv6.1 as a reference.

FIGURE 4

Number of homozygous and heterozygous deleterious alleles in each genome against DMv6.1 and RHv3.

FIGURE 5

Percentage of deleterious allele affected genes in 5 Mb bins of DMv6.1 in each genome. Black arrows over the x-axis indicate locations of the genes StCDF1 on chr05 and Sli on chr12.

FIGURE 6

Segregation distortion on chromosome 1 from a cross of 12120–03 × 07506–01. (A) Markers heterozygous in both parents were tested for deviation from the expected 1:2:1 segregation ratio of progeny using the chi-square test. The y-axis is the –log₁₀ Bonferroni adjusted p-value from the chi-square test for each of the markers. The x-axis shows the genome divided into 1 Mb bins which is labeled with the chromosome location-bin number. The -log10 adjusted p-value ≥ 1.2 was the threshold for segregation distortion. The arrow indicates the location of the solcap_snp_c2_14495 marker. This marker is in a gene that has two predicted deleterious alleles. (B) The region indicated by the arrow is shown in the DMv6.1 genome browser. (C) Progeny genotypes from a cross of 12120–03 × 07506–01. The solcap_snp_c2_14495 and solcap_snp_c1_4706 markers were adjacent to each other and both showed segregation distortion. The progeny genotype in the gray box has significantly reduced frequency compared to expected.

FIGURE 7

Insertion mutations of StCDF1 alleles. The location of KASP™ markers snpST00110 and snpST00091 are shown. The DNA binding domain is indicated in blue, GI binding domain is pink and FKF binding domain is purple.