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A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

Dadousis, Christos and Somavilla, Adriana and Ilska, Joanna J. and Johnsson, Martin and Batista, Lorena and Mellanby, Richard J. and Gottardo, Paolo and Headon, Denis and Whalen, Andrew and Wilson, David and Dunn, Ian C. and Gorjanc, Gregor and Kranis, Andreas and Hickey, John M. (2021). A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens. Genetics Selection Evolution. 53 , 70
[Research article]

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Abstract

Background: Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a "large" number of genes with "small" effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size.Methods: The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs.Results: GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67-66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained similar to 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (similar to 65.67-66.31 Mb).Conclusions: To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

Authors/Creators:Dadousis, Christos and Somavilla, Adriana and Ilska, Joanna J. and Johnsson, Martin and Batista, Lorena and Mellanby, Richard J. and Gottardo, Paolo and Headon, Denis and Whalen, Andrew and Wilson, David and Dunn, Ian C. and Gorjanc, Gregor and Kranis, Andreas and Hickey, John M.
Title:A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens
Series Name/Journal:Genetics Selection Evolution
Year of publishing :2021
Volume:53
Article number:70
Number of Pages:14
Publisher:BMC
ISSN:0999-193X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
URN:NBN:urn:nbn:se:slu:epsilon-p-113694
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113694
Additional ID:
Type of IDID
DOI10.1186/s12711-021-00663-w
Web of Science (WoS)000693813400001
ID Code:25493
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:23 Sep 2021 12:25
Metadata Last Modified:23 Sep 2021 12:31

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