GWLD: an R package for genome-wide linkage disequilibrium analysis

Abstract

Linkage disequilibrium (LD) analysis is fundamental to the investigation on genetic architecture of complex traits (e.g. human disease, animal and plant breeding), and population structure and evolution dynamics. However, until now, studies primarily focus on LD status between genetic variants located on the same chromosome. Moreover, genome (re-)sequencing produces unprecedented numbers of genetic variants, and fast LD computation becomes a challenge. Here, we have developed GWLD, a parallelized and generalized tool designed for the rapid genome-wide calculation of LD values, including conventional D/D’, r2 and (reduced) mutual information (MI and RMI) measures. LD between genetic variants within and across chromosomes can be rapidly computed and visualized in either R package or standalone C++ software. To evaluate the accuracy and speed of LD calculation, we conducted comparisons using four real datasets. Interchromosomal LD patterns observed potentially reflect levels of selection intensity across different species. Both versions of GWLD, the R package (https://github.com/Rong-Zh/GWLD-R) and the standalone C++ software (https://github.com/Rong-Zh/GWLD-C++), are freely available on GitHub.

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea

“…Therefore, LD analysis is a fundamental step in association analysis. The degree of LD between loci can be reflected in the D value and r 2 [51,52]. Qi et al [20] used SSR markers to analyze the linkage disequilibrium of barley populations and found that the range of D values was mainly concentrated between 0 and 0.6, accounting for 82.06% of the paired 992 SSR marker sites.…”