A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Abstract\ud \ud Background\ud Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds.\ud \ud \ud Results\ud ABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs.\ud \ud \ud Conclusions\ud This study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production.This study was supported by the Brazilian Agricultural Research Corporation\ud – Embrapa (project number 01.11.07.002.04.02) and by the thematic project\ud (2014/08704–0) from São Paulo Research Foundation (FAPESP). The TT Reference\ud Population was funded by the National Council of Scientific and Technological\ud Development (CNPq) grant number 481755/2007–1 from the Brazilian\ud Government. Boschiero received a fellowship from the program Science\ud Without Borders - CNPq, grant 370620/2013–5. G.C.M. Moreira received\ud fellowships from FAPESP, grants 14/21380–9 (in cooperation agreement\ud with CAPES), and 16/00569–1. T.F. Godoy received fellowship from FAPESP,\ud grant 15/00616–7 (in cooperation agreement with CAPES). L.L. Coutinho is\ud recipient of productivity fellowship from CNPq