Genetic diversity and phylogenetic relationships analyses of Taoyuan, Lanyu, and other exotic pig breeds based on mitochondrial sequences

Taoyuan pigs were introduced from Guangdong area in 1877 and were a major breed in early Taiwan. For improving their performance, Berkshire pigs were introduced into Taiwan by Japanese in 1896. Then according to their poor economic efficiency and lower willing of rearing, the number of pure Taoyuan pigs decreased dramatically after the exotic pig breeds (Yorkshire, Hampshire, Landrace, and Duroc) were introduced. For animal conservation, Taoyuan pigs were reared isolately in Taiwan Livestock Research Institute after 1974. Lanyu pigs, an indigenous breed in Lanyu Islet were transferred to National Taiwan University and Taitung Animal Propagation Station for developing laboratory swine in 1975 and 1980, respectively. Two herds of Lanyu pigs were reared in isolation and performed natural mating until 2004 and 1991. The genes of exotic pig breeds might introgress into Taoyuan and Lanyu pigs after exotic breeds introduced into Taiwan. The genetic diversity within conserved Taoyuan and Lanyu herds and whether the genetic introgression had previously occurred were currently unknown, so it is important identifying the genetic diversity of conserved herds for the orientation of conservation. he aims of the study were to investigate: (1) the genetic variation within conserved herds of Taoyuan and Lanyu pigs. (2) Whether the maternal genetic introgression from exotic pig breeds into the conserved herds (3) the phylogenetic relationships of two conserved breeds to worldwide pig breeds. The polymorphisms of mitochondrial sequences were applied for those studies. Mitochondrial DNAs of 129 individuals from Landrace, Yorkshire, Duroc, Berkshire, Meishan, and conserved herds of Taoyuan and Lanyu pigs were obtained. Their control region and cytochrome b fragments were amplified by polymerase chain reaction then sequenced. Genetic diversities within conserved herd sequences of Taoyuan and Lanyu pigs were examined based on the relationships of haplotype diversity (h) and nucleotide diversity (π). The Hasegawa-Kishino-Yano 85 (HKY85) substitution model was used to obtain the genetic distances based on the polymorphisms of substitution sites of control region and cytochrome b sequences. The Maximum Likelihood (ML) tree of different sequences was constructed according to the pairwise genetic distances. To determine the phylogenetic relationship among Taoyuan, Lanyu, and other Eurasian pig breeds, 55 control region sequences of Eurasian pig breed obtained from NCBI database were included.he control region and cytochrome b sequences of conserved Taoyuan only remained one haplotype, and shown absence of diversity by low h (0.000) and lowπ(0.000%) value; conserved Lanyu sequences were divided into two haplotypes (type I and type II), and shown severe loss of diversity by low h (0.384) and highπ(0.510%) value. In the phylogenetic relationship of control region and cytochrome b sequences, type I Lanyu formed a unique clade different from all other pigs while type II Lanyu sequence was clustered with Yorkshire, Berkshire, Meishan, and Taoyuan. In ML tree containing 184 control region sequences of Eurasian pigs, type I Lanyu sequence still formed a unique clade different from Asian and European pig sequences, while type II Lanyu and Taoyuan sequences were clustered within the Asian clade.n conclusion, low genetic diversity observed both in conserved Taoyuan and Lanyu pigs indicates recent population bottleneck or founder event might happen in these herds. Taoyuan sequence was clustered in Asian clade indicate that maternal lineage introgression from European clade pigs wasn’t found. Type I Lanyu sequence formed a unique clade different from other Asian and European sequences suggesting that the origin of Lanyu pigs have maternal lineage distinct from other Asian and European pigs. Type II Lanyu sequence was clustered within the Asian clade, it might be the result of maternal lineage introgression from Asian clade pigs into Lanyu pigs.