Wang Yuan, Dong Ruilan, Li Xiao, Cui Chao, Yu Guanghui
College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
Bureau of Agriculture and Rural Affairs of Jiaozhou, Jiaozhou 266300, China.
Animals (Basel). 2022 Apr 17;12(8):1045. doi: 10.3390/ani12081045.
The Licha black pig, a popular indigenous Chinese pig breed, is known for its multi-vertebral trait and higher lean meat rate. Understanding the current conservation status, family structure, and degree of inbreeding of the Licha black pig population will be useful to maintain a sufficient level of genetic diversity in these animal resources. In the present study, the genetic diversity, population structure, and inbreeding coefficient of this conserved population were analyzed using SNP genotyping data from 209 Licha black pigs. Based on the genomic information, this population was divided into eight different families with boars. The effective population size (N), polymorphic marker ratio (P), expected heterozygosity (H), and observed heterozygosity (H) of this population were 8.7, 0.827, 0.3576, and 0.3512, respectively. In addition, a total of 5976 runs of homozygosity (ROHs) were identified, and most of the ROHs (54.9%) were greater than 5 Mb. The genomic inbreeding coefficient of each individual was estimated based on ROHs () with an average inbreeding coefficient of 0.11 for the population. Five statistics (N, P, H, H, and ) showed a decrease in the level of genetic diversity and a high degree of inbreeding in this population. Thus, special preservation programs need to be implemented in the future, such as introducing new individuals or improving the mating plan. Altogether, our study provides the first genomic overview of the genetic diversity and population structure of Licha black pigs, which will be useful for the management and long-term preservation of this breed.
里岔黑猪是中国一种受欢迎的本土猪种，以其多脊椎性状和较高的瘦肉率而闻名。了解里岔黑猪群体的当前保护状况、家系结构和近亲繁殖程度，对于维持这些动物资源的足够遗传多样性水平将是有用的。在本研究中，利用来自209头里岔黑猪的单核苷酸多态性（SNP）基因分型数据，分析了这个保育群体的遗传多样性、群体结构和近亲繁殖系数。基于基因组信息，这个群体被分为八个不同的公猪家系。该群体的有效群体大小（N）、多态性标记比例（P）、期望杂合度（H）和观察杂合度（H）分别为8.7、0.827、0.3576和0.3512。此外，共鉴定出5976个纯合性片段（ROH），其中大多数ROH（54.9%）大于5兆碱基。基于ROH估计了每个个体的基因组近亲繁殖系数（），该群体的平均近亲繁殖系数为0.11。五个统计量（N、P、H、H和）表明该群体的遗传多样性水平下降且近亲繁殖程度较高。因此，未来需要实施特殊的保护计划，如引入新个体或改进交配计划。总之，我们的研究首次提供了里岔黑猪遗传多样性和群体结构的基因组概况，这将有助于该品种的管理和长期保护。
