Linkage disequilibrium maps in sub-Saharan African populations: gene essentiality and the interplay of selection, recombination and mutation

The extent and strength of linkage disequilibrium (LD) reflect the historical impact of recombination, selection and population history. The LD landscape in human population is known to comprise highly punctate hotspots that divide extended blocks of low haplotype diversity from narrow regions of LD breakdown. LD maps based on whole-genome sequence (WGS) data enables complete resolution of LD structure across human chromosomes. Increased marker density from WGS-derived data provides superior power for delineation of regions of the genome that are differentially recombined. We posited that recombination rate and haplotype diversity can be considered as a proxy for gene essentiality and establish the interesting relationship between gene function and LD strength. The weaker LD in sub-Saharan African population achieves unprecedented resolution for functional analysis LD maps in the context of human disorders.  We used Malécot-Morton model of LD to construct LD maps across six sub-Saharan African populations. The LD maps are constructed on the scale of linkage disequilibrium units (LDU) in which the decline of LD to ‘background’ levels across a variable physical distance corresponds to one LDU. The LDU scale enables direct comparison of the extent of LD in different genomic regions independent of the physical scale.