Liu Bin, Shen Linyuan, Guo Zhixian, Gan Mailing, Chen Ying, Yang Runling, Niu Lili, Jiang Dongmei, Zhong Zhijun, Li Xuewei, Zhang Shunhua, Zhu Li
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
Anim Biosci. 2021 Jul;34(7):1105-1115. doi: 10.5713/ajas.19.0884. Epub 2020 May 12.
To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study.
We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm.
The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (PN) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%.
This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure longterm preservation of Liangshan pig.
为了保护和利用中国地方传统猪种凉山猪的遗传资源，本研究评估了其遗传多样性、遗传结构和遗传距离。
我们使用50K单核苷酸多态性（SNP）芯片对凉山猪保种场的139头个体进行SNP检测。
这个遗传上封闭的保种群由五代重叠世代组成，群体的总有效含量（Ne）为15。整个群体分为五个公猪家系和一个非公猪家系。其中，各世代亚群体的有效规模持续下降。然而，多态性标记比例（PN）先下降后上升。这139头凉山猪的平均遗传距离为0.2823±0.0259，14头公猪的平均遗传距离为0.2723±0.0384。因此，可以推断遗传距离代代变化。在保种群中，检测到983个纯合片段（ROH），大多数ROH（80%）在100 Mb以内。基于ROH计算的全群近交系数平均值为0.026。此外，各世代亚群体的近交系数先上升后下降。在整个保种群的系谱中，父系信息错误率超过11.35%，而母系信息错误率超过2.13%。
这项对凉山猪群体遗传结构的分子研究表明，在封闭的跨世代繁殖过程中遗传多样性有所丧失。有必要改进配种计划或引入外来新血液以确保凉山猪的长期保存。
