Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array
Chicken carcass traits are economically important for the chicken industry. Detecting which genes affect chicken carcass traits is of great benefit to the genetic improvement of this important agricultural species. To investigate the genetic mechanism of carcass traits in chickens, we carried out a genome-wide association study (GWAS). A total of 435 Chinese indigenous chickens were phenotyped for carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW) after slaughter at 91 days and were genotyped using a 600-K single nucleotide polymorphism (SNP) genotyping array. Twenty-four birds were selected for sequencing, and the 600 K SNP panel data were imputed to sequence data with the 24 birds as the reference. Univariate GWASs were performed with GEMMA software using the whole genome sequence data imputed from SNP chip data. Finally, 3, 25, and 63 suggestively significant SNPs were identified to be associated with carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW), respectively. Six candidate genes, RNF219, SCEL, MYCBP2, ETS1, APLP2, and PRDM10 were detected. SCEL and MYCBP2 were potentially associated with these three traits, RNF219 and APLP2 were potentially associated with EWG and EW, and ETS1 and PRDM10 were only potentially associated with EWG and EW, respectively. Compared with forefathers’ research, 10 reported QTLs associated with CW were located within a 5-Mb distance near the SNPs with P value lower than 1×10−5. This study enriched the knowledge of the genetic mechanisms of chicken carcass traits.
KeywordsChicken GWAS Imputation Sequence data Carcass traits
This study was funded by the National Natural Science Foundation of China (31772556), the earmarked fund for China Agriculture Research System (CARS-41), the S&T Planning Project of Guangdong (2015A020209159), and the Pearl River S&T Nova Program of Guangzhou (201506010027).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
The experimental procedures used in this study met the guidelines of the Animal Care and Use Committee of the South China Agricultural University (SCAU) (Guangzhou, People’s Republic of China). All animal experiments of this study were approved by the Animal Care and Use Committee of the SCAU with approval number SCAU#0017. All efforts were made to minimize animal suffering.
- Bredrup C, Johansson S, Bindoff LA, Sztromwasser P, Krakenes J, Mellgren AE, Bruras KR, Lind O, Boman H, Knappskog PM, Rodahl E (2015) High myopia-excavated optic disc anomaly associated with a frameshift mutation in the MYC-binding protein 2 gene (MYCBP2). Am J Ophthalmol 159(5):973–979CrossRefPubMedGoogle Scholar
- Chen J, He T (2012) Factors affecting the accuracy of genotype imputation in populations from several maize breeding programs. Nat Struct Biol 9(10):729–733Google Scholar
- Madsen, P., P. Sørensen, G. Su, L. H. Damgaard, H. Thomsen and R. Labouriau (2006) DMU—a package for analyzing multivariate mixed models. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13–18 August, 2006Google Scholar
- Pertile SFN, Zampar A, Petrini J, Gaya LDG, Rovadoscki GA, Ramírezdíaz J, Ferraz JBS, Michelan Filho T, Mourão GB (2014) Correlated responses and genetic parameters for performance and carcass traits in a broiler line. Am J Hum Genet 15(4):1006–1016Google Scholar
- Turner SD (2014) qqman: an R package for visualizing GWAS results using QQ and manhattan plots. bioRxiv 005165Google Scholar