Zhao Qing-Bo, Sun Hao, Zhang Zhe, Xu Zhong, Olasege Babatunde Shittu, Ma Pei-Pei, Zhang Xiang-Zhe, Wang Qi-Shan, Pan Yu-Chun
Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.
Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.
Evol Bioinform Online. 2019 Jan 23;15:1176934318825082. doi: 10.1177/1176934318825082. eCollection 2019.
Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.05 were obtained for further analysis. In general, there are similar within-breed genetic diversities (He, Ho, P, A) among these 7 pig populations in the Taihu Lake region. Average values for the inbreeding coefficients estimates in the 7 populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen a continuous decline in Ne estimates over time with FJ and SW populations having a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection pressure than other Chinese pig breeds. The average genetic distances among the 7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269 (EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the number of haplotype blocks and haplotype diversity was also presented. This study provide a deep understanding of the current situation of conservation in this region, thereby uncovering the pertinent insight to better formulate more reasonable preservation policies for the government departments and breeding planners to follow-up.
太湖地区的中国本土猪以其高繁殖力和其他优良特性而闻名。为了更好地了解该地区这些品种的特性，并为政府和育种者提供制定合理保护政策的分子基础，我们利用下一代测序数据，探索了与这些重要遗传资源的管理和保护相关的7个群体的单倍型块结构和遗传多样性。在本研究中，共获得了131300个次要等位基因频率⩾0.05的单核苷酸多态性用于进一步分析。总体而言，太湖地区的这7个猪群体在品种内的遗传多样性（He、Ho、P、A）相似。7个群体中近亲繁殖系数估计值的平均值分别为0.110（F1）、0.056（F2）和0.078（F3）。随着时间的推移，所有品种的有效种群大小估计值都在持续下降，FJ和SW群体的曲线非常相似。此外，梅山猪品种的有效种群大小小于其他中国猪品种，这表明梅山猪品种比其他中国猪品种经历了更强的选择压力。太湖地区7个群体之间的平均遗传距离分别为0.235（MMS）、0.240（SMS）、0.269（EH）、0.248（MI）、0.221（FJ）、0.254（JX）和0.212（SW）。还给出了单倍型块数量和单倍型多样性的总结。本研究深入了解了该地区的保护现状，从而为政府部门和育种规划者更好地制定更合理的保护政策提供了相关见解以供后续参考。
