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Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach
BACKGROUND: Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performa...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836328/ https://www.ncbi.nlm.nih.gov/pubmed/31694549 http://dx.doi.org/10.1186/s12863-019-0783-3 |
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author | Moreira, Gabriel Costa Monteiro Poleti, Mirele Daiana Pértille, Fábio Boschiero, Clarissa Cesar, Aline Silva Mello Godoy, Thaís Fernanda Ledur, Mônica Corrêa Reecy, James M. Garrick, Dorian J. Coutinho, Luiz Lehmann |
author_facet | Moreira, Gabriel Costa Monteiro Poleti, Mirele Daiana Pértille, Fábio Boschiero, Clarissa Cesar, Aline Silva Mello Godoy, Thaís Fernanda Ledur, Mônica Corrêa Reecy, James M. Garrick, Dorian J. Coutinho, Luiz Lehmann |
author_sort | Moreira, Gabriel Costa Monteiro |
collection | PubMed |
description | BACKGROUND: Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F(2) Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. RESULTS: Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F(2) population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. CONCLUSIONS: The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs. |
format | Online Article Text |
id | pubmed-6836328 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-68363282019-11-08 Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach Moreira, Gabriel Costa Monteiro Poleti, Mirele Daiana Pértille, Fábio Boschiero, Clarissa Cesar, Aline Silva Mello Godoy, Thaís Fernanda Ledur, Mônica Corrêa Reecy, James M. Garrick, Dorian J. Coutinho, Luiz Lehmann BMC Genet Research Article BACKGROUND: Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F(2) Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. RESULTS: Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F(2) population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. CONCLUSIONS: The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs. BioMed Central 2019-11-06 /pmc/articles/PMC6836328/ /pubmed/31694549 http://dx.doi.org/10.1186/s12863-019-0783-3 Text en © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 Article Moreira, Gabriel Costa Monteiro Poleti, Mirele Daiana Pértille, Fábio Boschiero, Clarissa Cesar, Aline Silva Mello Godoy, Thaís Fernanda Ledur, Mônica Corrêa Reecy, James M. Garrick, Dorian J. Coutinho, Luiz Lehmann Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title | Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title_full | Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title_fullStr | Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title_full_unstemmed | Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title_short | Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
title_sort | unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836328/ https://www.ncbi.nlm.nih.gov/pubmed/31694549 http://dx.doi.org/10.1186/s12863-019-0783-3 |
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