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Genetic variation and phylogenetics of Lanyu and exotic pig breeds in Taiwan analyzed by 19 microsatellite markers

W. H. Cheng^*, H. P. Chu, Y. N. Jiang^*, S. H. Li, Y. Wang, C. H. Chen, K. J. Chen, C. Y. Lin^# and Y. T. Ju^*

^* Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan , Taitung Animal Propagation Station, Taitung, Taiwan , Department of Life Science, National Taiwan Normal University, Taipei, Taiwan , Livestock Research Institute, Tainan, Taiwan ^# Hualien Animal Propagation Station, Hualien, Taiwan

ytju{at}ntu.edu.tw

Abstract

The Lanyu pig is an indigenous miniature pig breed on Lanyu Islet near Taiwan, with a mitochondrial DNA genetic lineage remote from Asian and European pig breeds. The unknown population genetic structure and increased inbreeding among the small population of conserved Lanyu pigs is now of great conservation concern. Additionally, the presence for more than a century of exotic pig breeds in Taiwan has made gene introgression from exotic pig breeds into Lanyu pigs very possible. The present study thus aimed to investigate nuclear genetic variation within the conserved Lanyu pigs, and the phylogenetic relationship and possible genetic introgression between Lanyu and exotic pig breeds by determining the polymorphism of 19 microsatellite loci. In the Neighbor-Joining tree constructed from 7 pig breeds based on Cavalli-Sforza and Edward chord genetic distances, 3 major clades were recognized, where the Asian and European breeds were separately clustered into 2 clades with a 93.0 and 99.9% bootstrap confidence value, respectively. All individuals of the Lanyu breed formed a unique subclade within the Asian clade based on –ln(proportion of shared alleles), suggesting that the Lanyu breed possesses a unique nuclear genetic structure and that no nuclear gene introgression from exotic breeds into the conserved Lanyu pigs has occurred in recent history. Fifteen of 19 microsatellite loci deviated from Hardy-Weinberg equilibrium (by Wright's statistic), suggesting a significant loss of heterozygosity in the conserved population. The valuable nuclear genetic structure and phylogenetic information should assist future conservation and population management of Lanyu pigs.

Key Words: genetic variation • introgression • Lanyu breed • microsatellite • phylogenetics • pig • Taiwan