College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Equine Center, China Agricultural University, Beijing 100193, China.
Genes (Basel). 2022 Mar 28;13(4):603. doi: 10.3390/genes13040603.
In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of were significantly increased among the different heat shock durations. The expression level of and declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse.
在本研究中，使用 Illumina Equine SNP70 Bead Array 对来自 10 个中国本土马品种的 301 个样本进行了全基因组 CNV 检测，并鉴定和验证了与金马适应高温高湿有关的候选基因。我们总共确定了 31 对常染色体上大小为 1.06 Kb 至 2023.07 Kb 的 577 个 CNV。通过聚合每个品种的重叠 CNV，在 10 个中国马品种中总共检测到 495 个 CNVR。确定了多达 211 个品种特异性 CNVR，其中 64 个在金马群体中发现。通过去除品种间重复的 CNV 区域，在中国本土马品种中共鉴定出 239 个 CNVR，包括 102 个缺失、133 个增益和 4 个两者（同一区域的缺失和增益），其中 131 个 CNVR 是新的，仅在本研究中检测到，而在以前的研究中没有检测到。总检测到的 CNVR 长度为 41.74Mb，占马常染色体总长度的 1.83%。CNVR 在每条染色体上的覆盖率从 0.47%到 15.68%不等，在 ECA12 上的覆盖率最高，但在 ECA1 和 ECA24 上检测到的 CNVR 数量最多。在中国东南沿海特有的、具有高温高湿适应性的金马种群中，共检测到 229 个与 CNVR 重叠的基因。对这些基因的功能注释表明，它们与细胞热适应和免疫有显著关系。通过对马成纤维细胞进行不同时间的热休克处理，验证了候选基因的表达水平。结果表明，在不同的热休克时间下，的表达水平显著增加。和的表达水平从热休克开始到热休克 2 小时后下降，然后逐渐增加，分别在热休克 6 小时和 10 小时达到最高值。本研究揭示了中国本土马品种的品种特异性 CNVR，这有助于对整个基因组进行 CNV 作图，并为金马适应高温高湿的分子机制提供了有价值的见解。
