Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle

Prasad, Aparna; Schnabel, Robert D.; McKay, Stephanie; Murdoch, Brenda M.; Stothard, Paul; Kolbehdari, D.; Wang, Z.; Taylor, Joseph J.; Moore, S. S.

doi:10.1111/j.1365-2052.2008.01772.x

Cited by 40 publications

(34 citation statements)

References 34 publications

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“…Quantitative trait loci influencing beef production have been previously reported in these regions. Prasad et al (2008) examined allelic frequencies of Holsteins and Angus for 355 and 175 SNPs on BTA19 and -29, respectively. They reported 14 regions with large differences between the two breeds.…”

Section: Resultsmentioning

confidence: 99%

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

et al. 2010

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The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals. The validity of this approach was confirmed by obtaining extremely large CLLs at the sites of causative variation for polled (BTA1) and black-coat-color (BTA18) phenotypes. Across the 30 bovine chromosomes, 699 putative selection signatures were detected. The largest CLL was on BTA6 and corresponded to KIT, which is responsible for the piebald phenotype present in four of the five dairy breeds. Potassium channel-related genes were at the site of the largest CLL on three chromosomes (BTA14, -16, and -25) whereas integrins (BTA18 and -19) and serine/arginine rich splicing factors (BTA20 and -23) each had the largest CLL on two chromosomes. On the basis of the results of this study, the application of population genomics to farm animals seems quite promising. Comparisons between breed groups have the potential to identify genomic regions influencing complex traits with no need for complex equipment and the collection of extensive phenotypic records and can contribute to the identification of candidate genes and to the understanding of the biological mechanisms controlling complex traits.

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Section: Resultsmentioning

confidence: 99%

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

et al. 2010

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“…This estimate was later supported by Kim and Kirkpatrick (2009) and now by our results. McKay et al (2007), Prasad et al (2008) and Sargolzaei et al (2008) arrived at completely different conclusions. They claimed that the minimum array for association study should consist of SNPs , 70 kbp apart.…”

Section: Discussionmentioning

confidence: 95%

Population parameters incorporated into genome-wide tagSNP selection

Silesian

Szyda

2013

Animal

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Single nucleotide polymorphisms (SNPs) are the most widespread source of variation in genomes. While the very large number of SNPs allows for a very precise description of genetic variation, it impedes data processing and significantly increases analysis time. Many of the SNPs located close to each other frequently carry the same or similar information. This problem can be solved by selecting the most informative SNPs (tagSNPs) using linkage disequilibrium information by identifying a set of tagSNPs representative for a chromosome fragment. The goal of this study is to check whether the genetic structure of a population, expressed by relationship and inbreeding coefficients, affects tagSNP selection. Six subsets of 450 bulls are selected out of the 1228 Polish Holstein-Friesian bulls genotyped by the Illumina BovineSNP50 Bead Chip. TagSNPs are selected for each of the subsets, as well as for the whole data set. The average reduction of the SNP number is 77.2% and is very similar in each sub-population. Differences in tagSNP selection between sub-populations are small. On average, 93.88% of the tagSNPs overlap between subsets. The study showed that differences in the genetic structure of the reference population have little influence on tagSNP selection.

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“…Assuming that pedigrees were complete, coancestry was rather small but still might lead to bias in the estimation of the disequilibria currently present in the Australian dairy population. The square of the correlation of alleles at two loci (r 2 ) has been widely used in animals with a half-sib structure to estimate linkage disequilibrium (McKay et al 2007;de Roos et al 2008;Hayes et al 2008;Prasad et al 2008;Sargolzaei et al 2008;Bovine Hap Map Consortium 2009;Kim and Kirkpatrick 2009;Qanbari et al 2010). Most of these studies identify phased haplotypes using available information from pedigrees.…”

Section: Discussionmentioning

confidence: 99%

Maximum Likelihood Estimation of Linkage Disequilibrium in Half-Sib Families

Gomez‐Raya

2012

Genetics

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Maximum likelihood methods for the estimation of linkage disequilibrium between biallelic DNA-markers in half-sib families (half-sib method) are developed for single and multifamily situations. Monte Carlo computer simulations were carried out for a variety of scenarios regarding sire genotypes, linkage disequilibrium, recombination fraction, family size, and number of families. A double heterozygote sire was simulated with recombination fraction of 0.00, linkage disequilibrium among dams of d= 0.10, and alleles at both markers segregating at intermediate frequencies for a family size of 500. The average estimates of d were 0.17, 0.25, and 0.10 for Excoffier and Slatkin (1995), maternal informative haplotypes, and the half-sib method, respectively. A multifamily EM algorithm was tested at intermediate frequencies by computer simulation. The range of the absolute difference between estimated and simulated d was between 0.000 and 0.008. A cattle half-sib family was genotyped with the Illumina 50K BeadChip. There were 314,730 SNP pairs for which the sire was a homo-heterozygote with average estimates of r 2 of 0.115, 0.067, and 0.111 for half-sib, Excoffier and Slatkin (1995), and maternal informative haplotypes methods, respectively. There were 208,872 SNP pairs for which the sire was double heterozygote with average estimates of r 2 across the genome of 0.100, 0.267, and 0.925 for half-sib, Excoffier and Slatkin (1995), and maternal informative haplotypes methods, respectively. Genome analyses for all possible sire genotypes with 829,042 tests showed that ignoring half-sib family structure leads to upward biased estimates of linkage disequilibrium. Published inferences on population structure and evolution of cattle should be revisited after accommodating existing half-sib family structure in the estimation of linkage disequilibrium.

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Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle

Cited by 40 publications

References 34 publications

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

Population parameters incorporated into genome-wide tagSNP selection

Maximum Likelihood Estimation of Linkage Disequilibrium in Half-Sib Families

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