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LD estimation and LD decay

PR Pablo Federico Roncallo
AL Adelina Olga Larsen
AA Ana Laura Achilli
CP Carolina Saint Pierre
CG Cristian Andrés Gallo
SD Susanne Dreisigacker
VE Viviana Echenique
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Linkage disequilibrium (LD) was calculated in the TASSEL 5.0 software [97] considering only SNPs with an MAF > 0.05 to avoid a bias effect of the LF SNPs on LD [98]. LD was measured as the allele frequency correlation (r2) for all pairwise SNP comparison in each chromosome and subsequently the chromosome and genome specific mean values were estimated. Inter-chromosomic LD (unlinked loci) was estimated over the whole genome. The LD decay was determined by plotting the r2 values against the genetic distance of loci pairs (Mb) for each chromosome and a trend line describing the LD decay was calculated by locally-weighted polynomial regression (LOESS) in R (http://www.r-project.org). The 95th percentile of the distribution of square root transformed inter-chromosomal LD values (r2) [99] was estimated as the critical threshold below which the LD could be considered as being caused by physical linkage. The intersection point between the LD curve and the r2 threshold determined the LD decay value for each chromosome.

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