Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle

BMC Genetics

Rong-Cai Yang¹  Stephen S Moore²  Zhiquan Wang²  Qi Jiang² 

[1] Research and Innovation Division, Alberta Agriculture and Rural Development, Edmonton, Alberta, T6H 5T6, Canada;Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada

关键词: Zygotic linkage disequilibrium;    Genome-wide multilocus structure;    Gametic linkage disequilibrium;    Crossbred cattle;   

Others  :  1122436
DOI  :  10.1186/1471-2156-13-65

 received in 2011-12-13, accepted in 2012-07-06,  发布年份 2012

【 摘 要 】

Background

Linkage 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.

Results

This 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.

Conclusions

This 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.

【 授权许可】

   
2012 Jiang et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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