Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders

Background Aim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to provide a list with implicated candidate genes for the trait. A number of 2586 female broilers genotyped with the high density (~ 600 k) SNP array and with records on EN (mean = 132.4 eggs, SD = 29.8 eggs) were used. Data were analyzed with application of additive and dominant multi-locus mixed models. Results A number of 7 additive, 4 dominant and 6 additive plus dominant marker-trait significant associations were detected. A total number of 57 positional candidate genes were detected within 50 kb downstream and upstream flanking regions of the 17 significant markers. Functional enrichment analysis pinpointed two genes ( BHLHE40 and CRTC1 ) to be involved in the ‘entrainment of circadian clock by photoperiod’ biological process. Gene prioritization analysis of the positional candidate genes identified 10 top ranked genes ( GDF15, BHLHE40, JUND, GDF3, COMP, ITPR1, ELF3, ELL, CRLF1 and IFI30). Seven prioritized genes ( GDF15, BHLHE40, JUND, GDF3, COMP, ELF3, CRTC1) have documented functional relevance to reproduction, while two more prioritized genes ( ITPR1 and ELL ) are reported to be related to egg quality in chickens. Conclusions Present results have shown that detailed exploration of phenotype-marker associations can disclose the mode of action of genetic variants and help in identifying causative genes associated with reproductive traits in the species.