15
Haplotype diversity analysis in ten US cattle breeds
Linkage disequilibrium (LD) between SNP markers is commonly reported in scientific publications because it may reflect the extent of linkage phase between QTL and SNP marker, which is fundamental information for association studies and genomic selection. Some studies have demonstrated that SNP in strong LD are organized into discrete blocks or haplotypes, which may be separated by recombination hot spots. Haplotypes are of direct scientific interest as they may be in perfect LD with QTL alleles, and they cause the observed LD between SNP markers. In this study, we reconstructed haplotypes within each 1-Mb SNP window for 10 US cattle breeds genotyped with the Illumina BovineSNP50K. Then, we investigated the diversity of common haplotypes, which we defined as those that were observed at a frequency of at least 1 in 100 in each breed. The average number of common haplotypes across the entire genome was 18 and ranged from 15~25 in individual breeds. Some specific windows showed consistent increased or decreased haplotype diversity in all breeds. Low haplotype diversity was observed in some windows of most chromosomes for all the breeds. This information provides direction for future studies to characterize haplotype diversity in relation to annotated gene-rich regions, published QTL, selection signals and loss-of-function mutations.
Keywords:
haplotype diversity, linkage disequilibrium, beef cattle