Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers

Abstract

The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that have been analyzed so far for the extent of LD, cultivated potato (Solanum tuberosum L.), an outcrossing species, is a highly heterozygous autotetraploid. The favored genotypes of modern cultivars are maintained by vegetative propagation through tubers. As a first step in the LD analysis, we surveyed both coding and noncoding regions of 66 DNA fragments from 47 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with experimental SNP detection. The total length of all analyzed fragments was >25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (=11.5x10(-3)) and diversity (pi=14.6x10(-3)) was high compared to the other plant species. The overall Tajima's D value (0.5) was not significant, but indicates a deficit of low-frequency alleles relative to expectation. To eliminate the possibility that an elevated D value occurs due to population subdivision, we assessed the population structure with probabilistic statistics. The analysis did not reveal any significant subdivision, indicating a relatively homogenous population structure. However, the analysis of individual fragments revealed the presence of subgroups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show relatively fast decay of LD in the short range (r2=0.208 at 1 kb) but slow decay afterward (r2=0.137 at approximately 70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of approximately 10 cM. We speculate that two conflicting factors play a vital role in shaping LD in potato: the outcrossing mating type and the very limited number of meiotic generations.

Figure 1.—

Distribution of (A) nucleotide polymorphism (θ × 10⁻³), (B) nucleotide diversity (π × 10⁻³), (C) Tajima's D, and (D) linkage disequilibrium (r²) within 100 bp (LD₁₀₀) in the surveyed fragments.

Figure 2.—

Decay of linkage disequilibrium (r²) as a function of distance between two polymorphic sites. Pooled data from all surveyed fragments were used to estimate the (A) short-range (≤1 kb) and (B) long-range linkage disequilibrium. Note that distances for the long-range LD are in kilobase pairs (kb) and centimorgans (cM). The last column indicates LD between polymorphic loci from different chromosomes.

Figure 3.—

Inferred population structure for the set of potato accessions. (A) Results based on SNPs from all surveyed fragments. (B) Results based on SNPs from the BA121o1-T7 fragment only. Q statistics indicate the proportion of an accession's genome that belongs to the first of two possible subgroups (K = 2).