Location of the Larger Linkage Disequilibrium Blocks in the Mexican and North American Holstein Cattle

Genomic selection relies on linkage between Quantitative Trait Loci (QTL) and genetic markers, but being in linkage disequilibrium (LD) in one population, will not necessarily imply that the markers are in LD in other populations. The objective of this study was to find the larger blocks which are in LD in the Mexican and North American Holstein populations and search for regions related to previous genome annotations. The analysis included information of 149 and 173 unrelated animals from the Mexican and North American Holstein populations respectively. After quality control, a total of 6,1847 SNP markers were included in the analysis. LD between the SNP markers was calculated through the use of r², using the SVS Golden Helix software, and the blocks were referenced to the cattle QTLdb. The largest block markers in LD in the populations were located in chromosomes 3, 7, 8, 9, 12, 14, 16 and 20, and the LD blocks included 640, 1358, 241, 188, 221, 321, 611 and 317 Kb in each chromosome respectively. Seven of the eight LD regions have been related to 65 association studies or QTL identifications in Holstein cattle. Of all references, 3 are related to health traits, 45 to milk composition, 10 to milk yield and 7 to fertility traits. The LD region of chromosome 8 has not been referenced previously for association or QTL. Traits referenced in the LD regions, could explain the genetic selection background. Conservation of LD regions in both populations could help to improve the genomic selection of Holstein cattle in Mexico.