Genomic regions associated with individual growth and cage feed efficiency in rabbits under two feeding regimes

Our objective was to identify genomic regions associated with individual growth (ADGf), and cage feed intake (FIf), feed conversion ratio (FCRf) and residual feed intake (RFIf) in ad libitum-fed rabbits; as well as with individual growth (ADGr) in rabbits fed under restriction. Three genome-wide association methods were used to analyze the aforementioned traits on 438 rabbits genotyped for 114,604 SNPs. The methods were: i) regression on each SNP allele counting (Reg), ii) bivariate animal model between the performance trait and each SNP allele counting (Bi) and iii) random QTL model combining LD and linkage information (LDLA). LDLA returned the largest number of significant associations. Bi and Reg yielded significant associations only at chromosome (Chr) level. At this level, LDLA showed 22 chromosomal regions on Chr2, 3, 5, 6, 7, 9, 12, 14, 15, 18, 19 and 21 associated with ADGf. Reg yielded significant associations between ADGf and regions on Chr3, 5 and 21. Lastly, Bi revealed significant associations on Chr3, 5 and 16. All methods identified the region 102-113 Mb on Chr3 as significantly associated with ADGf. At Chr5, the 19-20 Mb region was associated with ADGf by Reg and Bi, while the 34-35 Mb region was associated with ADGf by Bi and LDLA. One region (0-2 Mb) on Chr13 and two regions (29-32 Mb and 38-39 Mb) on Chr9 were significantly associated with ADGr by Reg and Bi methods, respectively. Bi, the only method used to analyze traits recorded at cage level, revealed significant associations between FIf and region 3-4 Mb on Chr5, and between RFIf and regions Chr8:108-110 Mb and Chr21:7-8 Mb. No significant associations were identified for FCRv. A total of 36 chromosome regions were significantly associated with the traits under study, one of them (Chr21:7-8 Mb) having pleiotropic effect on ADGf and RFIf. After gene and functional annotation, 29 candidate genes on 22 out of these 36 significant regions were identified. It is remarkable that one of the identified candidate genes (FTO) was previously associated with growth in rabbits. In addition, candidate genes FEZF2 and PTPRG for ADGr, are involved in the control of feeding behavior traits.