Abstract
BackgroundLinkage disequilibrium (LD) between genes at linked or independent loci can occur at gametic and zygotic levels known asgametic LD and zygotic LD, respectively. Gametic LD is well known for its roles in fine-scale mapping of quantitative trait loci, genomic selection and evolutionary inference. The less-well studied is the zygotic LD and its components that can be also estimated directly from the unphased SNPs.ResultsThis study was set up to investigate the genome-wide extent and patterns of zygotic LD and its components in a crossbred cattle population using the genomic data from the Illumina BovineSNP50 beadchip. The animal population arose from repeated crossbreeding of multiple breeds and selection for growth and cow reproduction. The study showed that similar genomic structures in gametic and zygotic LD were observed, with zygotic LD decaying faster than gametic LD over marker distance. The trigenic and quadrigenic disequilibria were generally two- to three-fold smaller than the usual digenic disequilibria (gametic or composite LD). There was less power of testing for these high-order genic disequilibria than for the digenic disequilibria. The power estimates decreased with the marker distance between markers though the decay trend is more obvious for the digenic disequilibria than for high-order disequilibria.ConclusionsThis study is the first major genome-wide survey of all non-allelic associations between pairs of SNPs in a cattle population. Such analysis allows us to assess the relative importance of gametic LD vs. all other non-allelic genic LDs regardless of whether or not the population is in HWE. The observed predominance of digenic LD (gametic or composite LD) coupled with insignificant high-order trigenic and quadrigenic disequilibria supports the current intensive focus on the use of high-density SNP markers for genome-wide association studies and genomic selection activities in the cattle population.
Highlights
Linkage disequilibrium (LD) between genes at linked or independent loci can occur at gametic and zygotic levels known asgametic LD and zygotic LD, respectively
Zygotic LD and its components The estimates of power of chi-square tests for zygotic LD and individual genic disequilibria were plotted against the marker distances of ≤ 50 Mega base pairs (Mb) for all single nucleotide polymorphism (SNP) pairs on 29 autosomes (Figure 1)
The trigenic and quadrigenic disequilibria were not shown because there was little trend of decay for these disequilibria even within 5 Mb
Summary
Linkage disequilibrium (LD) between genes at linked or independent loci can occur at gametic and zygotic levels known asgametic LD and zygotic LD, respectively. The gametic LD cannot be calculated directly for unphased SNP markers because the gametic phase of animals that are heterozygous at two or more loci cannot be directly observed or specified. These studies have often followed the classic approach of Hill [9] to estimating gametic LD for unphased data, but such estimation was carried out under the assumption of Hardy-Weinberg equilibrium (HWE). The animals in this study are the progenies of three synthetic lines that were maintained separately at the University of Alberta Kinsella Research Ranch during 1960 to 1989 [10] and were subsequently pooled It will hereafter be called as the Kinsella composite beef population. There is a need to examine the dependence of zygotic LD and its components on gene frequencies
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