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A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations

Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)-analysis is a...

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Autores principales: Riggio, V, Pong-Wong, R, Sallé, G, Usai, MG, Casu, S, Moreno, CR, Matika, O, Bishop, SC
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BlackWell Publishing Ltd 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258091/
https://www.ncbi.nlm.nih.gov/pubmed/24397290
http://dx.doi.org/10.1111/jbg.12071
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author Riggio, V
Pong-Wong, R
Sallé, G
Usai, MG
Casu, S
Moreno, CR
Matika, O
Bishop, SC
author_facet Riggio, V
Pong-Wong, R
Sallé, G
Usai, MG
Casu, S
Moreno, CR
Matika, O
Bishop, SC
author_sort Riggio, V
collection PubMed
description Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)-analysis is a tool for aggregating information from multiple independent studies. The aim of this study was to identify loci underlying variation in FEC, as an indicator of nematode resistance, in a joint analysis using data from three populations (Scottish Blackface, Sarda × Lacaune and Martinik Black-Belly × Romane), genotyped with the ovine 50k SNP chip. The trait analysed was the average animal effect for Strongyles and Nematodirus FEC data. Analyses were performed with regional heritability mapping (RHM), fitting polygenic effects with either the whole genomic relationship matrix or matrices excluding the chromosome being interrogated. Across-population genomic covariances were set to zero. After quality control, 4123 animals and 38 991 SNPs were available for the analysis. RHM identified genome-wide significant regions on OAR4, 12, 14, 19 and 20, with the latter being the most significant. The OAR20 region is close to the major histocompatibility complex, which has often been proposed as a functional candidate for nematode resistance. This region was significant only in the Sarda × Lacaune population. Several other regions, on OAR1, 3, 4, 5, 7, 12, 19, 20 and 24, were significant at the suggestive level.
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spelling pubmed-42580912014-12-11 A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations Riggio, V Pong-Wong, R Sallé, G Usai, MG Casu, S Moreno, CR Matika, O Bishop, SC J Anim Breed Genet Original Articles Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)-analysis is a tool for aggregating information from multiple independent studies. The aim of this study was to identify loci underlying variation in FEC, as an indicator of nematode resistance, in a joint analysis using data from three populations (Scottish Blackface, Sarda × Lacaune and Martinik Black-Belly × Romane), genotyped with the ovine 50k SNP chip. The trait analysed was the average animal effect for Strongyles and Nematodirus FEC data. Analyses were performed with regional heritability mapping (RHM), fitting polygenic effects with either the whole genomic relationship matrix or matrices excluding the chromosome being interrogated. Across-population genomic covariances were set to zero. After quality control, 4123 animals and 38 991 SNPs were available for the analysis. RHM identified genome-wide significant regions on OAR4, 12, 14, 19 and 20, with the latter being the most significant. The OAR20 region is close to the major histocompatibility complex, which has often been proposed as a functional candidate for nematode resistance. This region was significant only in the Sarda × Lacaune population. Several other regions, on OAR1, 3, 4, 5, 7, 12, 19, 20 and 24, were significant at the suggestive level. BlackWell Publishing Ltd 2014-12 2014-01-08 /pmc/articles/PMC4258091/ /pubmed/24397290 http://dx.doi.org/10.1111/jbg.12071 Text en © 2014 The Authors. Journal of Animal Breeding and Genetics Published by Blackwell Verlag GmbH http://creativecommons.org/licenses/by/3.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Articles
Riggio, V
Pong-Wong, R
Sallé, G
Usai, MG
Casu, S
Moreno, CR
Matika, O
Bishop, SC
A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title_full A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title_fullStr A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title_full_unstemmed A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title_short A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
title_sort joint analysis to identify loci underlying variation in nematode resistance in three european sheep populations
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258091/
https://www.ncbi.nlm.nih.gov/pubmed/24397290
http://dx.doi.org/10.1111/jbg.12071
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