A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits

SIMPLE SUMMARY: Rabbit meat has been widely consumed in China and is considered as an ideal food source due to its high protein, low fat, low cholesterol and low sodium contents. The growth rate, carcass characteristics and meat quality are considered economically important traits in the rabbit industry. Genomic selection (GS) could facilitate genetic selection for important economic traits, however, the lack of molecular markers for these traits limits the application of GS in rabbits. Genome-wide association study (GWAS) has the potential to comprehensively identify trait-associated molecular markers and has been applied in animal and plant research. In this study, GWAS was used to examine growth, carcass and meat quality traits of meat rabbits based on specific-locus amplified fragment sequencing (SLAF-seq) technology to identify significantly associated SNPs and functional genes, to be used as a basis for prompting the application of GS in rabbits. ABSTRACT: Growth, carcass characteristics and meat quality are the most important traits used in the rabbit industry. Identification of the candidate markers and genes significantly associated with these traits will be beneficial in rabbit breeding. In this study, we enrolled 465 rabbits, including 16 male Californian rabbits and 17 female Kangda5 line rabbits as the parental generation, along with their offspring (232 male and 200 female), in a genome-wide association study (GWAS) based on SLAF-seq technology. Bodyweight at 35, 42, 49, 56, 63 and 70 d was recorded for growth traits; and slaughter liveweight (84 d) and dressing out percentage were measured as carcass traits; and cooking loss and drip loss were measured as meat quality traits. A total of 5,223,720 SLAF markers were obtained by digesting the rabbit genome using RsaI + EcoRV-HF(®) restriction enzymes. After quality control, a subset of 317,503 annotated single-nucleotide polymorphisms (SNPs) was retained for subsequent analysis. A total of 28, 81 and 10 SNPs for growth, carcass and meat quality traits, respectively, were identified based on genome-wide significance (p < 3.16 × 10(−7)). Additionally, 16, 71 and 9 candidate genes were identified within 100 kb upstream or downstream of these SNPs. Further analysis is required to determine the biological roles of these candidate genes in determining rabbit growth, carcass traits and meat quality.