Research on Linkage Disequilibrium Method Based on OpenMP

Abstract

Linkage disequilibrium method is applied for the research on inferring population genetics, LD mapping, haploid type diversity analysis and so on. Soybean genotypes are adopted as the data source and linkage disequilibrium parallel algorithm is implemented by OpenMP technology. In this algorithm, single nucleotide polymorphism sites are divided by using sliding windows into groups, adjacent sites allele in a window of each chromosome are parallel calculated and store the LD results. According to the experimental data, the serial and parallel algorithms are compared and analyzed. The conclusion shows that the OpenMP parallel technology can effectively improve the efficiency of linkage disequilibrium analysis method. It is a realistic significance for processing massive biological information data.