Genetic Variations within the Bovine CRY2 Gene Are Significantly Associated with Carcass Traits

SIMPLE SUMMARY: Carcass traits are crucial for beef cattle breeding. CRY2, as a clock gene, affects the body’s metabolism and regulates the physiological function of skeletal muscles, including muscle growth and development. In order to investigate the relationship between the CRY2 gene and cattle carcass traits, a total of 705 individuals from the Shandong Black Cattle Genetic Resource (SDBCGR) population were randomly collected. Eight potential insertion/deletion sites within the CRY2 gene were analyzed, and two of them were polymorphic. Population genetic parameters including genotype frequencies and allele frequencies of the two loci in the tested population were calculated. Importantly, the two loci were significantly related to carcass traits such as gross weight, ribeye, and high rib, suggesting that CRY2 shows the potential for bovine growth and development. The two loci can be used as effective molecular markers affecting carcass traits of beef cattle and provide certain scientific and theoretical bases for practical breeding. ABSTRACT: As an important part of the circadian rhythm, the circadian regulation factor 2 of cryptochrome (CRY2), regulates many physiological functions. Previous studies have reported that CRY2 is involved in growth and development. However, the relationship between CRY2 gene polymorphism and cattle carcass traits remains unclear. The aim of this study was to detect the possible variations of the CRY2 gene and elucidate the association between the CRY2 gene and carcass traits in the Shandong Black Cattle Genetic Resource (SDBCGR) population (n = 705). We identified a 24-bp deletion variation (CRY2-P6) and a 6-bp insertion variation (CRY2-P7) in the bovine CRY2 gene. The frequency of the homozygous II genotype is higher than the heterozygous ID genotype in both two loci. In addition, CRY2-P6 was consistent with HWE (p > 0.05). Importantly, the CRY2-P6 variant was significantly associated with 12 carcass traits, including gross weight, ribeye, high rib, thick flank, etc. and the II was the dominant genotype. The CRY2-P7 site was also significantly correlated with five traits (gross weight, beef-tongue, etc.). Collectively, these outcomes indicated that the two Indel loci in the CRY2 gene could be used for marker-assisted selection of cattle carcass traits.