School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China.
Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, P.R. China.
BMC Genomics. 2021 Mar 2;22(1):151. doi: 10.1186/s12864-021-07476-7.
China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation.
In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig. Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds.
Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future.
中国是世界上拥有最丰富猪遗传资源的国家。经过数千年的驯化和自然选择，中国的大多数猪都形成了独特的遗传特征。寻找每个品种的独特遗传特征和模块是其精确保护的重要组成部分。
本研究采用偏最小二乘法鉴定了 19 个中国地方猪种和 5 个西方猪种的显著特异性 SNPs。从这些品种中获得了 37514 个显著特异性 SNPs（p<0.01），具有最多显著 SNPs 的中国本地猪种是 Hongdenglong（HD），其次是 Jiaxing black（JX）、Huaibei（HB）、Bihu（BH）、小型梅山（SMS）、Shengxian Hua（SH）、Jiangquhai（JQ）、Mi（MI）、Chunan（CA）、Chalu（CL）、Jinhualiangtouwu（JHL）、Fengjing（FJ）、中梅山（MMS）、Shanzhu（SZ）、Pudong white（PD）、Dongchuan（DC）、Erhualian（EH）、Shawutou（SW）和 Lanxi Hua（LX）猪。此外，我们使用 KOBAS 和 IPA 鉴定了具有最显著基因、GO 术语、途径和网络的品种，并分别对其进行了排名。结果表明，具有最多互作网络的品种是 Hongdenglong（12 个）和 Huaibei（12 个）猪。相比之下，互作网络最少的品种是 Shawutou（4 个）和 Lanxi Hua 猪（3 个），这表明 Hongdenglong 和 Huaibei 猪的基因组中可能具有最显著的遗传模块，而 Shawutou 和 Lanxi Hua 猪可能具有最不独特的特征。在某种程度上，鉴定出的特定途径和网络与特定品种相关的基因和 SNPs 数量有关，但它们似乎并不相同。最重要的是，在本地中国猪种中发现更多显著的模块与消化系统的发育和功能、疾病的调节以及氨基酸的代谢有关，而在西方猪种中发现更多显著的模块与生长速度有关。
我们的结果表明，每个品种都有一些相对独特的结构模块和功能特征。这些模块使我们能够更好地理解中国地方猪和西方猪种之间的遗传差异，从而实施精确的保护方法。本研究可为未来制定更有效的管理和保护这些遗传资源的策略提供依据。
