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Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle

Overview of attention for article published in BMC Genetics, February 2016
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Title
Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle
Published in
BMC Genetics, February 2016
DOI 10.1186/s12863-016-0339-8
Pubmed ID
Authors

Patrícia Biegelmeyer, Claudia C. Gulias-Gomes, Alexandre R. Caetano, Juan P. Steibel, Fernando F. Cardoso

Abstract

The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (N e ), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (R H,B ) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Mean LD estimates, measured using the squared correlation of alleles at two loci (r (2) ), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r (2) was > 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated N e for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (R H,B  = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (R H,B  = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r (2)  > 0.2) was found spanning to ~50 Kb. Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.

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Mendeley readers

The data shown below were compiled from readership statistics for 46 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 46 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 11 24%
Student > Ph. D. Student 10 22%
Student > Doctoral Student 7 15%
Researcher 6 13%
Student > Postgraduate 3 7%
Other 2 4%
Unknown 7 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 26 57%
Biochemistry, Genetics and Molecular Biology 5 11%
Veterinary Science and Veterinary Medicine 1 2%
Medicine and Dentistry 1 2%
Unknown 13 28%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 February 2016.
All research outputs
#5,062,308
of 7,089,314 outputs
Outputs from BMC Genetics
#416
of 647 outputs
Outputs of similar age
#202,709
of 320,347 outputs
Outputs of similar age from BMC Genetics
#31
of 49 outputs
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