PSVIII-31 Genome-wide estimation of linkage disequilibrium using American mink genotyping-by-sequencing data

Abstract

Abstract Linkage disequilibrium (LD) has been defined as the correlation between alleles at different loci in the genome. The LD levels can be influenced by the evolutionary processes and historical events in populations. The main objective of this study was to estimate the LD levels at different distances of American mink genome using genotyping-by-sequencing (GBS) data. A total of 285 American mink (Neovison vison) were sequenced based on GBS libraries prepared by digesting the genomic DNA with the restriction enzyme ApeKI. After quality control, 13,321 single nucleotide polymorphism (SNP) markers located on 46 Scaffolds were used to determine the extension of LD in the genome. The average r2 was computed for all syntenic SNP pairwise at inter-marker distances from 0 up to 1 Mb. The average r2 between adjacent SNPs was 0.29, ranged from 0.18 to 0.53 across all scaffolds. In addition, the average distance between adjacent markers was 51 kb. The average r2 above 0.3 was observed in less than 1 kb distances and declined with increase in distances between markers. The average r2 was estimated to be less than 0.2 for markers more than 10 kb apart. Furthermore, the average LD level was decreased to 0.08 for inter-marker distances between 0.9 and 1 Mb. The results of this study can be used to determine the optimum maker density required for obtaining enough accuracy and power in both genomic selection and genome-wide association studies.