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The LD method is based on the following relationship for unlinked loci, as assumed here (Hill 1981), E (r 2 ′ ) ≈ 1 (3 N e ), so N ^ b = 1 (3 r 2 ′ ), (3)where r2′ is the squared correlation of alleles at different loci and is an index of the amount of disequilibrium due to drift, after accounting for effects of sampling.
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The degree of genetic isolation would have implications for using this germplasm for association studies, since a higher amount of linkage disequilibrium (LD) would be predicted within an isolated group, making whole genome LD scans more feasible.
The markers contributing to the positive relationship between heterozygosity and breeding success were found to be located on different chromosomes, but there was a substantial amount of linkage disequilibrium in the population, indicating that the markers are reflecting heterozygosity over relatively wide genomic regions.
The amount of linkage disequilibrium (D) between selected loci is measured after dispersal at the center of the overlapping clines.
The magnitude of indirect effects depends on the amount of linkage disequilibrium and therefore on selection, recombination, and dispersal.
The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome.
The accuracy of genomic prediction with Bayesian models is lower in populations with a large effective population size and thus a low amount of linkage disequilibrium [ 4].
Statistical power in GWAS is a function of odds ratios and the amount of linkage disequilibrium between causal alleles and marker alleles.
We observed 23 haplotypes involving alleles at these loci and a large amount of linkage disequilibrium between alleles (Additional file 1, table S3).
We have also estimated the amount of linkage disequilibrium (LD) between the two ESR1 SNPs separated by about 140 kb on chromosome 6 and investigated their haplotype effect on breast cancer using the software "Unphased" from Dudbridge [ 51].
These involve thousands and for some species hundreds of thousands of SNPs approximately equally spaced across the genome, to capture the greatest amount of linkage disequilibrium with causative QTL.
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