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Linkage disequilibrium in crossbred and pure line chickens

BACKGROUND: Both genome-wide association (GWA) studies and genomic selection depend on the level of non-random association of alleles at different loci, i.e. linkage disequilibrium (LD), across the genome. Therefore, characterizing LD is of fundamental importance to implement both approaches. In thi...

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Autores principales: Fu, Weixuan, Dekkers, Jack CM, Lee, William R, Abasht, Behnam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341223/
https://www.ncbi.nlm.nih.gov/pubmed/25887184
http://dx.doi.org/10.1186/s12711-015-0098-4
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author Fu, Weixuan
Dekkers, Jack CM
Lee, William R
Abasht, Behnam
author_facet Fu, Weixuan
Dekkers, Jack CM
Lee, William R
Abasht, Behnam
author_sort Fu, Weixuan
collection PubMed
description BACKGROUND: Both genome-wide association (GWA) studies and genomic selection depend on the level of non-random association of alleles at different loci, i.e. linkage disequilibrium (LD), across the genome. Therefore, characterizing LD is of fundamental importance to implement both approaches. In this study, using a 60K single nucleotide polymorphism (SNP) panel, we estimated LD and haplotype structure in crossbred broiler chickens and their component pure lines (one male and two female lines) and calculated the consistency of LD between these populations. RESULTS: The average level of LD (measured by r(2)) between adjacent SNPs across the chicken autosomes studied here ranged from 0.34 to 0.40 in the pure lines but was only 0.24 in the crossbred populations, with 28.4% of adjacent SNP pairs having an r(2) higher than 0.3. Compared with the pure lines, the crossbred populations consistently showed a lower level of LD, smaller haploblock sizes and lower haplotype homozygosity on macro-, intermediate and micro-chromosomes. Furthermore, correlations of LD between markers at short distances (0 to 10 kb) were high between crossbred and pure lines (0.83 to 0.94). CONCLUSIONS: Our results suggest that using crossbred populations instead of pure lines can be advantageous for high-resolution QTL (quantitative trait loci) mapping in GWA studies and to achieve good persistence of accuracy of genomic breeding values over generations in genomic selection. These results also provide useful information for the design and implementation of GWA studies and genomic selection using crossbred populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0098-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-43412232015-02-27 Linkage disequilibrium in crossbred and pure line chickens Fu, Weixuan Dekkers, Jack CM Lee, William R Abasht, Behnam Genet Sel Evol Research BACKGROUND: Both genome-wide association (GWA) studies and genomic selection depend on the level of non-random association of alleles at different loci, i.e. linkage disequilibrium (LD), across the genome. Therefore, characterizing LD is of fundamental importance to implement both approaches. In this study, using a 60K single nucleotide polymorphism (SNP) panel, we estimated LD and haplotype structure in crossbred broiler chickens and their component pure lines (one male and two female lines) and calculated the consistency of LD between these populations. RESULTS: The average level of LD (measured by r(2)) between adjacent SNPs across the chicken autosomes studied here ranged from 0.34 to 0.40 in the pure lines but was only 0.24 in the crossbred populations, with 28.4% of adjacent SNP pairs having an r(2) higher than 0.3. Compared with the pure lines, the crossbred populations consistently showed a lower level of LD, smaller haploblock sizes and lower haplotype homozygosity on macro-, intermediate and micro-chromosomes. Furthermore, correlations of LD between markers at short distances (0 to 10 kb) were high between crossbred and pure lines (0.83 to 0.94). CONCLUSIONS: Our results suggest that using crossbred populations instead of pure lines can be advantageous for high-resolution QTL (quantitative trait loci) mapping in GWA studies and to achieve good persistence of accuracy of genomic breeding values over generations in genomic selection. These results also provide useful information for the design and implementation of GWA studies and genomic selection using crossbred populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0098-4) contains supplementary material, which is available to authorized users. BioMed Central 2015-02-26 /pmc/articles/PMC4341223/ /pubmed/25887184 http://dx.doi.org/10.1186/s12711-015-0098-4 Text en © Fu et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Fu, Weixuan
Dekkers, Jack CM
Lee, William R
Abasht, Behnam
Linkage disequilibrium in crossbred and pure line chickens
title Linkage disequilibrium in crossbred and pure line chickens
title_full Linkage disequilibrium in crossbred and pure line chickens
title_fullStr Linkage disequilibrium in crossbred and pure line chickens
title_full_unstemmed Linkage disequilibrium in crossbred and pure line chickens
title_short Linkage disequilibrium in crossbred and pure line chickens
title_sort linkage disequilibrium in crossbred and pure line chickens
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341223/
https://www.ncbi.nlm.nih.gov/pubmed/25887184
http://dx.doi.org/10.1186/s12711-015-0098-4
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