State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China.
Department of Animal Science, Jiangxi Biotech Vocational College, 330200, Nanchang, China.
Anim Genet. 2018 Aug;49(4):275-283. doi: 10.1111/age.12687.
Dongxiang Spotted, Pingxiang Two-End-Black and Yushan Black pigs are three indigenous breeds in Jiangxi Province, China, that have been listed in the national conservation program for Chinese indigenous livestock germplasm. Here, we investigated the genetic diversity and population structure of the nucleus populations of these three breeds in a worldwide context of European and Chinese pigs using Illumina Porcine 60K chips. Our data indicate that Dongxiang Spotted and Yushan Black pigs have recently experienced severe inbreeding. The two breeds show large runs-of-homozygosity values, long-range extents of linkage disequilibrium and reduced observed heterozygosity. In contrast, Pingxiang Two-End-Black pigs are rich in genetic diversity and have few inbred individuals. Both phylogenetic and admixture analyses illustrate that Dongxiang Spotted and Yushan Black pigs are genetically close to their geographical neighbors in East China and that Pingxiang Two-End-Black pigs have a close relationship with three other Two-End-Black breeds in central China. Finally, we reconstructed the family structures of the three breeds and propose a reliable breeding strategy to better conserve these breeds.
东乡花猪、萍乡两头乌猪和玉山黑猪是中国江西省的三个本土品种，已被列入中国本土家畜遗传资源保护计划。在这里，我们使用 Illumina Porcine 60K 芯片，在全球范围内调查了这三个品种的核心群体的遗传多样性和群体结构。我们的数据表明，东乡花猪和玉山黑猪最近经历了严重的近交。这两个品种表现出较大的纯合子 Runs 值、长程连锁不平衡和降低的观测杂合度。相比之下，萍乡两头乌猪遗传多样性丰富，近交个体较少。系统发育和混合分析都表明，东乡花猪和玉山黑猪在遗传上与华东地区的地理邻居密切相关，而萍乡两头乌猪与中国中部的另外三个两头乌猪品种密切相关。最后，我们重建了这三个品种的家系结构，并提出了一个可靠的繁殖策略，以更好地保护这些品种。
