Genome wide association study for egg defects in layer chickens

Egg defects in layers are responsible for income losses for the poultry industry and represent a potential hazard for food safety. The objective of this study was to find genomic regions associated with various egg defects in layers in order to improve efficiency of selection against egg defects. The proportions of eggs that had calcium deposits (CD), were broken (BK), dirty (DE), double yolked (DY), misshaped (ME), soft-shelled (SS) and shell-less (SL) was analyzed for 11,445 hens from 6 generations. The information included individual performance for 1,412 genotyped hens and 1,536 phenotypic family means of genotyped parents. After quality control 24,383 SNPs were used. Method BayesCPi was used to fit all markers simultaneously. The genome was represented as 1 Mb windows. The proportion of genetic variance explained by each window and the proportion of iterations of the MCMC chain in which it was included in the model were used as criteria to determine the regions of the genome most strongly associated with the analyzed traits. Average frequency of defects was low: BK 0.5%, CD 1.1%, DE 0.3%, DY 0.6%, ME 0.3%, SL 0.2%, SS 0.2%. The following chromosomes were found to contain genomic regions associated with egg defects BK 1,3,4,Z,20; CD 2,5,7,15; DE 3,12; DY 1,3,4,6; ME 1,2,4,5; SL 1,3,4,14; SS 1,4,26,Z. In conclusion, the study has detected a number of genomic regions showing association with egg defects, some of which explain a sizeable proportion of genetic variance. Funded by USDA NIFA AFRI Award 2010-65205-20341 and the EW group.