Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
Anim Genet. 2020 Dec;51(6):940-944. doi: 10.1111/age.12993. Epub 2020 Aug 17.
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 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.
通城猪和大白猪之间存在较大的表型差异。然而，其遗传基础知之甚少。本研究利用基因组测序数据，对通城猪和大白猪的 CNVs 进行了全基因组比较。通过结合三种不同策略（读深度、配对末端映射和分裂读）的优势，我们总共检测到了 18687 个 CNVs，覆盖了通城猪和大白猪基因组长度的约 3.5%。我们通过 V 统计对 1864 个品种分层 CNVs（前 10%）进行了鉴定。位于品种分层 CNVs 中的基因的功能富集分析发现，这些基因参与了色素沉着、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。利用对基因组和转录组数据的系统分析，我们进一步鉴定了四个新的功能基因上的品种差异 CNVs（抗病基因、DCUN1D2 和 SPARCL1；脂质代谢基因、PLEKHA2 和 SLCO1A2）。随后的 PCR 验证证实了它们在 33 头通城猪和 33 头大白猪中的准确断点位置。本研究为进一步研究通城猪和大白猪表型差异的遗传基础提供了差异 CNVs 的重要信息。
