Abstract：
This study aimed to evaluate the impact of copy number variants (CNVs) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing Log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole genome sequence data from 126 animals, resulting in 870 high-confidence CNV regions (CNVRs) on 12,131 animals. Out of these, 54 CNVRs had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVRs were significantly (p-value < 3.7 × 10-5) associated with at least one of the traits analyzed in this study. Specifically, 2 CNVRs were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and non-return rate), and 2 CNVRs were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVRs harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVRs on the mentioned traits are warranted.
摘要：
本研究旨在评估拷贝数变异（CNVs）对荷斯坦牛13种繁殖和12种疾病性状的影响。强度信号文件包含来自13,730只荷斯坦动物的LogR比率和B等位基因频率信息，用95KSNP面板进行基因分型，和8,467只具有50KSNP组基因分型的荷斯坦动物用于鉴定CNV。随后，使用来自126只动物的全基因组序列数据验证鉴定的CNV，在12,131只动物上产生870个高置信度CNV区域（CNVR）。在这些中，54个CNVR在人群中的频率高于或等于1％，并用于全基因组关联分析（一次一个CNVR，包括G矩阵)。结果显示,4个CNVR与本研究中分析的至少一个性状显著相关(p值<3.7×10-5)。具体来说,2个CNVR与3个繁殖性状相关(即，小牛生存,第一个服务概念，和无退货率)，和2个CNVR与2个疾病性状相关(即，子宫炎和胎盘保留）。这些CNVRs包含与免疫反应有关的基因，细胞信号，和神经元发育，支持他们在这些特征中的潜在参与。有必要进行进一步的研究，以揭示这些CNVR对上述特征的机理和功能影响。
