Abstract: Aspects of the present invention provide novel compositions and methods based on novel calpastatin (CAST) genetic markers, such as missense mutations in exon 3 that result in G48D or P52L substitutions (NM_174003.2:c.271G>A and 283C>T), a G/T substitution in intron 3 (AAFC02060381.1:g.2110G>T) and a GAAA repeat in intron 8 (AAFC02060381.1:g.6700[(GAAA)4]+[(GAAA)5]. Particular aspects provide novel markers for fertility (e.g., daughter pregnancy rate, DPR) and longevity (e.g., productive life, PL) in, for example, dairy cattle. Additional aspects provide for novel methods comprising marker-assisted selection to improve fertility and/or longevity in dairy cattle. Therefore, in particular embodiments, a combination of genetic selection based on one or more of the novel CAST markers, and high PTA potentials of milk production traits, provides for improved reproductive traits in association with continued high milk production traits.

Abstract: Aspects of the present invention also provide novel compositions and methods based on novel CRH single nucleotide polymorphisms selected from the group consisting of AAFC03076794.1:g.9657C>T, c.10718G>C, c.10841G>A, c.10893A>C and c.10936G>C, which may provide novel markers for marbling and/or subcutaneous fat depth. Additional aspects provide for novel methods which may comprise marker-assisted selection or marker-assisted management to improve marbling and/or subcutaneous fat depth in cattle.

Abstract: Particular aspects provide an inexpensive QTL mapping approach for genome-wide scans of QTL linked markers and for narrowed locations of QTL regions, which may comprise integration of the amplified fragment length polymorphism (AFLP) with DNA pooling and selective genotyping and comparative bioinformatics tools. AFLP simultaneously screens high numbers of loci for polymorphisms and detects many more polymorphic DNA markers than any other PCR based detection systems, and provides for identification of “responsible mutations” for a QTL. Aspects of the present invention also provide novel compositions and methods based on novel DOPEY2 and/or KIAA1462 single nucleotide polymorphisms such as AAFC03071397.1:g.12881G>C, g.12925G>A, g.12951T>C, g.13013A>G, g.13125G>A and g.13173C>T in the DOPEY2 gene and AAFC02113318.1:g.1367G>A and g.1372G>A in the KIAA1462 gene, which may provide novel markers for beef marbling and subcutaneous fat.

Abstract: The physiological regulation of intake, growth and energy partitioning in animals is under the control of multiple genes, which may be important candidates for unraveling the genetic variation in economically relevant traits in beef production. The present invention relates to the identification of single nucleotide polymorphisms (SNPs) within the bovine genes encoding fatty acid binding proteins and their associations with economically relevant traits in beef production. The invention further encompasses methods and systems, including network-based processes, to manage the SNP 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.