Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes1

Tenesa, Albert; Knott, Sara; Ward, Daniel; Smith, Deborah L.; Williams, John L.; Visscher, Peter M.

doi:10.2527/2003.813617x

Cited by 63 publications

(74 citation statements)

References 21 publications

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“…This statistic has been used to measure the extent of LD in human [3] and livestock populations in a range of studies (e.g. [10,28,34,42]), thereby facilitating the comparison of the results in this study with other studies. D allows LD to be measured with highly polymorphic markers and is less sensitive to variation in marker allele frequencies than other measures of LD [14,46].…”

Section: Estimating Linkage Disequilibrium Between Pairs Of Markersmentioning

confidence: 99%

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Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Khatkar¹,

Thomson²,

Tammen³

et al. 2006

Genet. Sel. Evol.

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-We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D . Estimates of D from the two approaches were in close agreement (r = 0.91). The mean estimates of D for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (∼37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.linkage disequilibrium / dairy cattle / markers / chromosome 6

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Section: Estimating Linkage Disequilibrium Between Pairs Of Markersmentioning

confidence: 99%

“…These studies used family information to infer the most likely phase of the dams' haplotypes. Tenesa et al [42] reported some evidence of LD on BTA6 in a sample of unrelated United Kingdom dairy cattle. Sutter et al [41] used several samples of unrelated animals to estimate LD in a range of dog breeds.…”

Section: Introductionmentioning

confidence: 99%

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Khatkar¹,

Thomson²,

Tammen³

et al. 2006

Genet. Sel. Evol.

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“…LD mapping has been used extensively to identify genes for monogenic diseases in humans (Peltonen 2000). Contrary to the situation in humans, extensive LD over a long range was observed in dairy cattle, sheep, and pigs (Farnir et al 2000;Mcrae et al 2002;Tenesa et al 2003;Nsengimana et al 2004;Harmegnies et al 2006) because of limited effective population sizes. Thus, LD mapping in livestock, and in other populations with (historically) limited effective population sizes, might be effective using marker maps of more limited density than what is required for most human populations because of the extensive LD that is created by drift in populations of limited effective sizes (Terwilliger et al 1998;Farnir et al 2002).…”

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confidence: 99%

Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci

2007

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Linkage disequilibrium (LD) analysis in outbred populations uses historical recombinations to detect and fine map quantitative trait loci (QTL). Our objective was to evaluate the effect of various factors on power and precision of QTL detection and to compare LD mapping methods on the basis of regression and identity by descent (IBD) in populations of limited effective population size (N e ). An 11-cM region with 6-38 segregating single-nucleotide polymorphisms (SNPs) and a central QTL was simulated. After 100 generations of random mating with N e of 50, 100, or 200, SNP genotypes and phenotypes were generated on 200, 500, or 1000 individuals with the QTL explaining 2 or 5% of phenotypic variance. To detect and map the QTL, phenotypes were regressed on genotypes or (assumed known) haplotypes, in comparison with the IBD method. Power and precision to detect QTL increased with sample size, marker density, and QTL effect. Power decreased with N e , but precision was affected little by N e . Single-marker regression had similar or greater power and precision than other regression models, and was comparable to the IBD method. Thus, for rapid initial screening of samples of adequate size in populations in which drift is the primary force that has created LD, QTL can be detected and mapped by regression on SNP genotypes without recovering haplotypes.

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“…Additionally, until recently most studies have focused on bovine populations from developed 1 countries where they are subjected to intensive breeding, such as the Holstein breed, and these studies have suggested that significant LD among markers extends over several megabases (Farnir et al 2000;Tenesa et al 2003;Khatkar et al 2006;Thevenon et al 2007). As part of the whole bovine genome sequencing project, significant efforts are currently being carried out to identify a large number of SNPs by comparing hundreds of thousands of random sequences originating from a small set of individuals belonging to different populations with a reference sequence.…”

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confidence: 99%

Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

et al. 2007

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To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances (,10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of ,300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds.

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Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes1

Cited by 63 publications

References 21 publications

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci

Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

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