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

Christos Dadousis, Adriana Somavilla, Joanna Ilska, Martin Johnsson, Lorena Batista, Richard Mellanby, Denis Headon, Paolo Gottardo, Andrew Whalen, David Wilson, Ian Dunn, Gregor Gorjanc, Andreas Kranis, John Hickey

Research output: Contribution to journalArticlepeer-review

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 SNP.
Results
GWAS revealed 25 genome regions harbouring 96 significant SNPs on 13 Gallus
gallus autosomes (GGA 1–4, 8,10-15, 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, and 13–14); (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) (both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined, the 25 genome regions harbouring the 96 significant SNPs explained ~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 (~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. Despite the identified regions, which showed a strong
association with BW, a high proportion of genetic variance attributed to regions
harbouring non-significant SNP 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.
Original languageEnglish
Pages (from-to)70
JournalGenetics Selection Evolution
Volume53
Issue number1
Early online date8 Sep 2021
DOIs
Publication statusE-pub ahead of print - 8 Sep 2021

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