Du Huipeng, Hu Jianchao, Zhang Zhiyan, Wu Zhongzi
National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330029, China.
Animals (Basel). 2025 Feb 19;15(4):603. doi: 10.3390/ani15040603.
Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs.
猪是重要的家畜，在众多猪品种中，中国本土品种梅山猪以其高繁殖性能而闻名。该品种已被引入许多国家以加强当地的猪育种计划。然而，针对梅山猪的基因组和群体遗传学研究有限。我们利用从一头梅山猪收集的高深度PacBio测序和Illumina测序数据创建了一个染色体水平的基因组组装。此外，我们分析了中国公猪和梅山猪的全基因组测序（WGS）数据，以确定梅山猪品种内的驯化选择信号。发现梅山猪（MSjxau）的组装基因组大小为2.45 Gb，支架长度为139.17 Mb。质量值为37.06，BUSCO评分96.2%，表明具有良好的完整性、连续性和准确性。我们对MSjxau基因组中的转座元件、片段重复和基因进行了注释。通过将这些数据与28个公开可用的基因组相结合，我们为猪提供了高质量的结构变异资源。此外，我们确定了中国野猪和梅山猪之间716个选择性清除区间，其中所选基因可能与梅山猪的高繁殖力有关。我们的研究为猪育种提供了有价值的基因组和变异资源，并鉴定了几个与梅山猪驯化相关的基因。这为进一步研究猪复杂性状背后的遗传机制奠定了基础。
