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

TCAP, TNNI1, and FHL1 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 TCAP, TNNI1, and FHL1 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 TCAP, TNNI1, and FHL1 genes were exclusively expressed in muscle tissue. These data support the high potentials of the TCAP, TNNI1, and FHL1 as marker genes to improve the growth performance and carcass quality traits of Qinchuan cattle or other animals selection programs.

TCAP、TNNI1及FHL1调控肌肉生长发育。本研究以576头肉牛为研究对象，采用混合DNA测序（DNA pooled sequencing）、聚合酶链式反应-限制性片段长度多态性（polymerase chain reaction, PCR-RFLP）及强制PCR-RFLP技术，在TCAP、TNNI1及FHL1基因的几乎所有外显子与内含子区域内，共检测到4个单核苷酸变异（single nucleotide variants, SNVs）。4个单核苷酸变异均与肉牛的生长性能及胴体品质性状呈显著相关。此外，本研究还在该试验牛群体中评估了3个序列变异的单倍型（haplotype）、单倍型频率（haplotype frequency）及连锁不平衡系数（linkage disequilibrium coefficient）。单倍型分析结果显示，秦川牛（Qinchuan cattle）群体中共存在8种单倍型，而中国荷斯坦奶牛（Chinese Holstein）群体中未检出单倍型；在秦川牛群体中，单倍型1的频率最高，达42.7%。对12种组合基因型的统计分析表明，部分组合基因型与秦川牛群体的生长性能及胴体品质性状显著相关。此外，实时荧光定量聚合酶链式反应（quantitative real-time polymerase chain reaction）结果证实，牛TCAP、TNNI1及FHL1基因仅在肌肉组织中特异性表达。本研究数据表明，TCAP、TNNI1及FHL1基因具备作为分子标记基因的较高潜力，可用于秦川牛或其他畜禽的遗传选育项目，以改良其生长性能与胴体品质性状。