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Content Provider | World Health Organization (WHO)-Global Index Medicus |
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Author | Qanbari, S. Pimentel, E. C. G. Tetens, J. Thaller, G. Lichtner, P. Sharifi, A. R. Simianer, H. |
Description | Country affiliation: Germany Author Affiliation: Qanbari S ( Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, 37075 Göttingen, Germany. sqanbar@gwdg.de) |
Abstract | This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r(2) statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r(2) = 0.30 +/- 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r(2) > or = 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < or =100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r(2). It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to approximately 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed. |
File Format | HTM / HTML |
ISSN | 02689146 |
Issue Number | 4 |
Volume Number | 41 |
e-ISSN | 13652052 |
Journal | Animal Genetics |
Language | English |
Publisher | Wiley-Blackwell |
Publisher Date | 2010-08-01 |
Publisher Place | Great Britain (UK) |
Access Restriction | Subscribed |
Subject Keyword | Discipline Genetics Discipline Zoology Cattle Genetics Linkage Disequilibrium Alleles Animals Genetic Variation Genetics, Population Genome-wide Association Study Haplotypes Polymorphism, Single Nucleotide Journal Article Research Support, Non-u.s. Gov't |
Content Type | Text |
Resource Type | Article |
Subject Domain (in MeSH) | Eukaryota Investigative Techniques Genetic Phenomena Natural Science Disciplines |
Subject | Animal Science and Zoology Genetics Medicine |
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