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Title: ASSESSMENT OF LINKAGE DISEQUILIBRIUM IN POTATO GENOME WITH SINGLE NUCLEOTIDE POLYMORPHISM MARKERS

Author
item SIMKO, IVAN - UNIV OF MARYLAND
item Haynes, Kathleen
item Jones, Richard

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2006
Publication Date: 8/1/2006
Citation: Simko, I., Haynes, K.G., Jones, R.W. 2006. Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics, vol. 173:pp. 1-9

Interpretive Summary: Potatoes are a major crop, providing food for millions and employment for thousands. The desirable modern potato has resulted from breeding of wild potato, which is poor yielding and misshapen. The desirable potato is maintained and multiplied by tubers, where genetic variation is halted. The genetic makeup of the modern potato was studied to develop ways of identifying genes that make modern potatoes better. Knowing the genes and how the genes are sorted out during breeding allows for further development of potato as a reliable food crop. Scientists will use this information to improve development of new varieties of potato.

Technical Abstract: The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that were so far analyzed 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 fragments from 46 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with the experimental SNP detection. The total length of all analyzed fragments was over 25 kb, and number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (' = 11.5 × 10-3) and diversity (' = 14.6 × 10-3) was relative high as 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 elevated D value occurs due to population subdivision, we assessed population structure with the probabilistic statistics. The analysis did not reveal any significant subdivision indicating a relative homogenous population structure. However, the analysis of individual fragments revealed a presence of sub-groups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show fast decay of LD at the short-range (r2 = 0.208 at 1 kb), but relatively slow decay afterward (r2 = 0.137 at ~70 kb). The estimate from the logarithmic regression model indicates that LD in potato declines below 0.20 at the distance of ~3 kb to ~5 kb. We speculate that the two conflicting factors play a vital role in shaping LD in potato; the outcrossing mating type and the very limited number of meiotic generations.