Sequence variants in the bovine silent information regulator 6, their linkage and their associations with body measurements and carcass quality traits in Qinchuan cattle

• We identified four novel SVs within bovine SIRT6.
• We analyzed the genotype distribution and genetic diversity four SVs within bovine SIRT6.
• Haplotype analyses of the four SVs were conducted.
• Effects of single markers/haplotype combinations on economic traits were analyzed in Qinchuan cattle.

Silent information regulator 6 (SIRT6) belongs to the family of class III nicotinamide adenine dinucleotide (NAD)-dependent deacetylase and plays an essential role in DNA repair and metabolism. This study was conducted to detect potential polymorphisms of the bovine SIRT6 gene and explore their relationships with body measurement and carcass quality in Qinchuan cattle. Four sequence variants (SVs) were identified in intron 6, exon 7, exon 9, and 3′ UTR, via sequencing technology conducted in 468 individual Qinchuan cattle. Eleven different haplotypes were identified, of which two major haplotypes had a frequency of 45.7% (–CACT–) and 14.8% (–CGTC–). Three SVs (SV2, SV3 and SV4) were significantly associated with some of the body measurements and carcass quality traits (P < 0.05 or P < 0.01), and the H2H7 (CC–GA–TT–TC) diplotype had better performance than other combinations. Our results suggest that some polymorphisms in SIRT6 are associated with production traits and may be used as candidates for marker-assisted selection (MAS) and management in beef cattle breeding programs.