Novel Muscle-Specific Genes <i>TCAP, TNNI1,</i> and <i>FHL1</i> in Cattle: SNVs, Linkage Disequilibrium, Combined Genotypes, Association Analysis of Growth Performance, and Carcass Quality Traits and Expression Studies

<i>TCAP, TNNI1,</i> and <i>FHL1</i> regulate muscle growth and development. In this study, four single nucleotide variants (SNVs) were discovered in almost all of the exon and intron regions of the <i>TCAP, TNNI1,</i> and <i>FHL1</i> genes using DNA pooled sequencing, polymerase chain reaction (PCR)-RFLP, and forced-PCR-RFLP methods in 576 cattle. Four SNVs were significantly associated with the growth performance and carcass quality traits of the cattle. In addition, the haplotype, haplotype frequency, and linkage disequilibrium coefficient of three sequence variants were also evaluated in the cattle population. Haplotype analysis demonstrated that eight haplotypes were present in the Qinchuan cattle population and no haplotypes were present in the Chinese Holstein population; haplotype 1 had the highest frequency in the Qinchuan (42.7%) population. Statistical analyses of 12 combined genotypes indicated that some were significantly associated with the growth performance and carcass quality traits of the Qinchuan cattle population. Moreover, the quantitative real-time polymerase chain reaction results demonstrated that the bovine <i>TCAP, TNNI1,</i> and <i>FHL1</i> genes were exclusively expressed in muscle tissue. These data support the high potentials of the <i>TCAP, TNNI1,</i> and <i>FHL1</i> as marker genes to improve the growth performance and carcass quality traits of Qinchuan cattle or other animals selection programs.