Linkage Disequilibrium and Haplotype Blocks in Cattle and Chicken Populations

Linkage disequilibrium (LD) using r² was studied in Italian Brown Swiss (BS) dairy cattle, a commercial broiler cross (BC), one brown-egg (BL) and two Leghorn layer (LLs) lines, using Illumina BovineSNP50K v1 and a custom 36K chicken SNP arrays. Datasets included non-redundant haplotypes (HTs) of the half-sib BS families, de-convoluted HTs of the BC parental lines, and genotypes of the layers. Non-syntenic (NS; from different chromosomes) SNP pairs were used to estimate LD distribution under the null hypothesis. Average population NS LD ranged from 0.004 to 0.045, depending on sample size and population. LD of all possible syntenic pairs was insensitive to sample size, averaging 0.016 for BS, 0.007 to 0.011 for BC, 0.016 for BL, and 0.030 and 0.056 for LLs. Diagonal LD averaged 0.254, 0.259 to 0.326, and 0.288, 0.537 and 0.844, respectively. HT blocks on a chromosome were identified based on all possible marker pairs, or on adjacent markers on the LD matrix diagonal. Two thresholds were used: r²=0.15 (close to the minimum for declaring significant LD), or r²=0.70 (minimum needed for effective whole genome association test). Blocks based on all pairs were fragmented and borders were harder to define than diagonal blocks. Acknowledgement. This study funded by EC (FP7/2007-2013), agreement n° 222664, “Quantomics” (this Publication reflects only the authors’ views and the EC is not liable for any use that may be made of the information contained herein). Hy-Line International, Aviagen and Italian Brown Cattle Breeders' Association provided data.