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

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.

Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits

“…Previously, Su et al discovered that an 18 bp deletion in intron 2 of PDGFD was associated with litter size for Australian white sheep [25]. Data from the Ruminant Genome and NCBI databases showed that PDGFD is highly expressed in the reproductive system (i.e., ovary) [25]. These results imply that PDGFD may control multiple traits simultaneously (i.e., gene pleiotropism).…”

“…Recently, Kang et al discovered that a 7 bp InDel variation in intron 8 of lysine demethylase 3B (KDM3B) not only affected the litter size of Australian white sheep, but was also significantly associated with the body size traits of Lanzhou fat-tailed sheep and Luxi black-headed sheep [41,42]. Previously, Su et al discovered that an 18 bp deletion in intron 2 of PDGFD was associated with litter size for Australian white sheep [25]. Data from the Ruminant Genome and NCBI databases showed that PDGFD is highly expressed in the reproductive system (i.e., ovary) [25].…”

“…On the basis of prior established formulas, body size indices, such as body trunk index (the ratio of chest circumference to body length), body length index (the ratio of body length to body height), chest width index (the ratio of chest width to chest depth), chest circumference index (the ratio of chest circumference to body height), cannon circumference index (the ratio of cannon circumference to body height), and limb length index (the ratio of the difference between body height and chest depth to body height), were also calculated [23,24]. Furthermore, genomic DNA was extracted from ear tissues using standard phenol/chloroform extraction procedures as described previously and diluted to 20 ng/µL with ddH 2 O after determination of concentration [25]. To study genetic differences in the PDGFD gene, 30 DNA samples from each sheep breed were chosen at random and placed into three different DNA pools [26][27][28].…”

“…These primers were synthesized via Sangon Biotech (Xi'an, Shaanxi, China). PCR was performed using a 13 µL reaction volume and Touchdown program described previously [25,26]. PCR products were then directly examined via electrophoresis with a 3% agarose gel for confirmation.…”

The ovine HIAT1 gene: mRNA expression, InDel mutations, and growth trait associations

“…Three upstream gene variants were screened from the Ensembl database, and then several primers ( Table 1 ) were designed using Primer Premier 5 software and synthesized by Sangon Biotech (Xi'an, China) based on reference sequences in ovine HIAT1 (NC 056054.1). Polymorphic fragments were amplified using the polymerase chain reaction (PCR) method and utilized a touch-down program and reaction volumes as described in previous studies ( 8 , 22 ). PCR products were then separated by electrophoresis on a 3.5% agarose gel stained with GoldView.…”