The present invention relates to the identification of single nucleotide polymorphisms (SNPs) in a ubiquinol-cytochrome c reductase core protein I (UQCRC1) gene and its associations association with fat deposition and fatty acid composition. The invention further encompasses methods and systems, including network-based processes, to manage the SNP data, haplotype data and other data relating to specific animals and herds of animals, veterinarian care, diagnostic and quality control data and management of livestock which, based on genotyping, have predictable meat quality traits, husbandry conditions, animal welfare, food safety information, audit of existing processes and data from field locations.
1. A method for identifying a bovine animal having a thinner subcutaneous fat depth (SFD), a lower skeletal muscle lipid accumulation (SMLA), a lower estimated stearoyl-CoA desaturase 16:1/16:0×100% value (R2), a lower estimated stearoyl-CoA desaturase 18:1/18:0×100% value (R3), a lower amount of beef fat monounsaturated fatty acids (MUFA), or a combination thereof, said method comprising:
(a) obtaining a biological sample from said bovine animal, said biological sample comprising nucleic acids encoding the bovine ubiquinol-cytochrome c reductase core protein I (UQCRC1) gene from said bovine;
(b) detecting in said nucleic acids the presence of at least one of:
(i) a C in at least one allele of the UQCRC1 gene at a position corresponding to 281 of SEQ ID NO: 1;
(ii) a C in both alleles of the UQCRC1 gene at a position corresponding to 281 of SEQ ID NO: 1;
(iii) a T in at least one allele of the UQCRC1 gene at a position corresponding to 465 of SEQ ID NO: 1; and
(iv) a T in both alleles of the UQCRC 1 gene at position corresponding to 465 of SEQ ID NO: 1; and
c) correlating the presence of the nucleic acid content detected in step (b) with a thicker SFD, a higher SMLA, a higher R2, a higher R3, a higher beef fat MUFA, or a combination thereof in said bovine animal, wherein:
the content detected in step (b)(i) is associated with lower R2, lower R3, and lower beef fat MUFA;
the content detected in step (b)(ii) is associated with thinner SFD and lower SMLA;
the content detected in step (b)(iii) is associated with lower R2, lower R3, and lower beef fat MUFA; and
the content detected in step (b)(iv) is associated with thinner SFD and lower SMLA.
2. A method for identifying a bovine animal having a thicker SFD, a higher SMLA, a higher R2), a higher R3, a higher amount of beef fat MUFA, or a combination thereof, said method comprising:
(a) obtaining a biological sample from said bovine animal, said biological sample comprising nucleic acids encoding the bovine UQCRC1 gene from said bovine;
(b) detecting in said nucleic acids the presence of at least one of:
(i) a T in both alleles of the UQCRC1 gene at a position corresponding to 281 of SEQ ID NO: 1
(ii) a T in at least one allele of the UQCRC1 gene at a position corresponding to 281 of SEQ ID NO: 1
(iii) a C in both alleles of the UQCRC1 gene at a position corresponding to 465 of SEQ ID NO: 1; and
(iv) a C in at least one allele of the UQCRC1 gene at position corresponding to 465 of SEQ ID NO: 1;
c) correlating the presence of the nucleic acid content detected in step (b) with a thicker SFD, a higher SMLA, a higher R2, a higher R3, a higher beef fat MUFA, or a combination thereof in said bovine animal, wherein:
the content detected in step (b)(i) is associated with higher R2, higher R3, and higher beef fat MUFA;
the content detected in step (b)(ii) is associated with thicker SFD and higher SMLA;
the content detected in step (b)(iii) is associated with higher R2, higher R3, and higher beef fat MUFA; and
the content detected in step (b)(iv) is associated with thicker SFD and higher SMLA.