Genome-wide linkage disequilibrium in South African abalone, Haliotis midae, and implications for understanding complex traits

Abstract

The abalone, Haliotis midae, is the most import aquaculture species in South Africa. Nonetheless, genetic improvement of the species is hindered by late maturity and long generational intervals. The application of marker assisted- and genomic selection is one strategy to accelerate genetic gains for production traits. However, with limited understanding of linkage disequilibrium, it is unclear how such a molecular-driven selective breeding approach should be implemented. The aim of this study was therefore to characterise LD in two wild and two cultured populations of the South African abalone and to investigate how their respective population histories have shaped LD across the genome and on a locus-specific scale. One hundred and twelve mapped microsatellite markers were used to genotype the four population cohorts. Levels of genetic diversity were similarly high for all cohorts, although significant population structure was evident. The decay of LD with genetic distance was present in both cultured cohorts, but almost absent within the wild cohorts. Levels of LD were high in comparison with other aquaculture species, but could be explained by various population demographic events related to the over-exploitation of the species in the wild, domestication, and the reproductive strategy of abalone. A number of interesting patterns were observed surrounding candidate loci under selection, including possible hitch-hiking events and epistatic interactions between loci. In terms of the potential for association studies, the persistence of significant LD over relatively long distances within these cohorts suggested that fewer markers would be sufficient to ensure marker-QTL co-segregation, although the use of generationally discrete cohorts is advised.