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doi:10.1534/genetics.106.060905
A more recent version of this article appeared on August 1, 2006.
REGULAR RESEARCH PAPERS |
Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers
Ivan Simko 1*, Kathleen G Haynes 1 and Richard W Jones 1
1 USDA-ARS
* To whom correspondence should be addressed. E-mail: isimko{at}pw.ars.usda.gov.
Submitted on May 16, 2006
Revised on June 8, 2006
Accepted on 12 June 2006
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 non-coding 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 over 25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (
= 11.5 X 10-3) and diversity (
= 14.6 X 10-3) 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 sub-groups 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 ~70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of ~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.
Key Words: Linkage disequilibrium, Population structure, Potato, Single nucleotide polymorphisms
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