Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome‐wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired‐end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed‐stratified CNVs (top 10%) by performing V_ST statistics. Functional enrichment analyses for genes located in breed‐stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed‐differential CNVs on the functional genes (disease‐resistant, DCUN1D2 and SPARCL1; lipid metabolism, PLEKHA2 and SLCO1A2). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.

中文翻译：

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全基因组测序揭示了桐城猪与大型白猪之间的不同品种CNV。

在桐城猪和大白猪之间已观察到较大的表型差异。但是，对其遗传基础知之甚少。这项研究使用基因组测序数据对通城猪和大白猪之间的CNV进行了全基因组比较。通过结合三种不同策略（读取深度，配对末端映射和拆分读取）的优势，我们检测到总共18687例CNV，覆盖了通城和大白猪的约3.5％的猪基因组长度。我们通过执行V _ST识别了1864个品种分层的CNV（前10％）统计。发现位于品种分层CNV中的基因的功能富集分析涉及色素沉着，行为，免疫系统和生殖过程，这与两个品种之间的表型差异相吻合。通过对基因组和转录组数据的系统分析，我们进一步鉴定了功能基因（疾病抗性，DCUN1D2和SPARCL1；脂质代谢，PLEKHA2和SLCO1A2）上的四个新的具有差异性的CNV。）。随后的PCR验证证实了它们在33头桐城猪和33头大白猪中的准确断点位置。这项研究提供了有关差异CNV的重要信息，以便进一步研究桐城猪与大白猪之间的表型差异的遗传基础。