Abstract：
Short interspersed nuclear elements (SINEs), one type of retrotransposon, are considered to be ideal molecular markers due to their wide distribution in the genome, high copy number, and high polymorphism. Preliminary studies have identified more than 35,000 SINE-retrotransposon insertion polymorphisms (RIPs) in the pig genome. In this study, 18 SINE-RIPs were used to evaluate the genetic variation and population structure of seven native pig populations and two crossbreeds in the Jiangsu Province of China. Two commercial pig breeds (Duroc and Large White) and one Italian native breed (Sicilian Black pig) were selected as the control. The results showed that all 18 SINE-RIPs were polymorphic among these pigs. The Jiangsu native pig populations (Erhualian, Fengjing, Middle Meishan, Mi, Shawutou, Small Meishan, and Huai) were shown to be more polymorphic than the crossbreeds (Sushan and Sujiang) and external breeds (Sicilian Black pig, Large White, and Duroc) based on the expected heterozygosity and polymorphic information content values. Some native pigs, including Small Meishan, Mi, Middle Meishan, and Erhualian, had a higher degree of inbreeding according to the FIS values. Based on the neighbor-joining tree, all of the Jiangsu native pig populations formed one branch, while the three external pig breeds formed the other branches, with the two crossbreeds containing more than 50% external pig ancestry. The Huai pigs were independent of the other Jiangsu native pigs but shared a common ancestor with Sujiang and Mi. The results provide a new perspective on the population structure of these native pig breeds and will assist with the conservation and utilization of Chinese native pigs.
摘要：
短散布核元素（SINE），一种反转录转座子,由于它们在基因组中的广泛分布，被认为是理想的分子标记，高拷贝数,和高度多态性。初步研究已经在猪基因组中鉴定了超过35,000个SINE-反转录转座子插入多态性(RIPs)。在这项研究中,18SINE-RIPs用于评估中国江苏省七个本地猪种群和两个杂交品种的遗传变异和种群结构。选择两个商业猪品种（Duroc和BigWhite）和一个意大利本地品种（西西里黑猪）作为对照。结果表明，所有18个SINE-RIP在这些猪中都是多态的。江苏土猪种群(二花莲，冯景,眉山中部,Mi,Shawutou,小梅山,和怀）被证明比杂交品种（苏山和苏江）和外部品种（西西里黑猪，大白色,和Duroc)基于预期杂合性和多态信息含量值。一些本地猪，包括小梅山，Mi,眉山中部,和Erhualian,根据FIS值，近亲繁殖程度更高。基于邻居连接树，所有江苏土猪种群组成一个分支，而三个外部猪品种形成了其他分支，这两个杂交品种含有50%以上的外部猪血统。淮猪独立于其他江苏土猪，但与苏江和米有共同的祖先。研究结果为这些地方猪品种的种群结构提供了新的视角，并将有助于中国地方猪的保护和利用。
