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

Dadousis, Christos (author), Somavilla, A. (author), Ilska, Joanna J. (author), Johnsson, Martin (author), Batista, Lorena G. (author), Mellanby, Richard J. (author), Headon, Denis (author), Gottardo, Paolo (author), Whalen, Andrew (author), Wilson, David (author), Dunn, Ian C. (author), Gorjanc, Gregor (author), Kranis, Andreas (author), Hickey, John M. (author)

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” efects is expected to control BW. To detect such efects, 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 signifcant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring signifcant SNPs (1 Mb up/downstream) and the combined regions harbouring non-signifcant SNPs. Results: GWAS revealed 25 genomic regions harbouring 96 signifcant 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 ~30% of the total genetic variance. The region harbouring signifcant 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. In spite of the identifed regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-signifcant 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.

• Language: English
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: Str. 1-14
• Numbering: Vol. 53, art. 70
• PID: 20.500.12556/RUL-132763
• UDC: 636.5:575
• ISSN on article: 1297-9686
• DOI: 10.1186/s12711-021-00663-w
• COBISS.SI-ID: 82665475
• Publication date in RUL: 02.11.2021

Record is a part of a journal

• Title: Genetics selection evolution
• Shortened title: Genet. sel. evol.
• Publisher: Springer Nature
• ISSN: 1297-9686
• COBISS.SI-ID: 3183636

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 08.09.2021

Secondary language

• Language: Slovenian
• Keywords: perutnina, kokoši, pitovni piščanci, telesna masa, genetika, genomika