Inter-population and intra-population maternal lineage genetics of Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences

¹ Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
² Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
³ Kaohsiung Animal Propagation Station, Livestock Research Institute, Kaohsiung, Taiwan
⁴ Department of Life Science, National Taiwan Normal University, Taipei, Taiwan

^* To whom correspondence should be addressed. E-mail: ytju{at}ntu.edu.tw.

	Abstract

The Lanyu pig is an indigenous breed from the Lanyu Islet, to the southeast of Taiwan. Two herds of Lanyu pigs were introduced from the Lanyu Islet into Taiwan in 1975 and 1980. The current population of conserved Lanyu pigs consists of only 44 animals with unknown genetic lineage. The Lanyu pig possesses a distinct maternal genetic lineage remote from Asian and European pigs. The present study aimed to understand the phylogenetic relationship among conserved Lanyu, Asian, and European type pigs based on the cytochrome b coding gene, to ascertain the maternal lineage and genetic diversity within the conserved Lanyu pigs, and to address whether genetic introgression from exotic or Formosan wild pigs had occurred in the conserved Lanyu pigs. The entire mitochondrial genomes of both types of Lanyu pig comprise 2 ribosomal RNAs, 22 tRNAs, and 13 protein-coding genes. Only 2 haplotypes of mitochondrial DNA control region and cytochrome b were identified in the conserved Lanyu pig herds. When Maximum Likelihood trees were constructed, the Type I Lanyu mitochondrial genes formed a unique clade with a large pairwise distance of both cytochrome b and control region from Asian and European type breeds, Formosan wild pigs, and exotic breeds. Significant loss of genetic diversity of mtDNAs within the conserved Lanyu pigs was demonstrated by low haplotype and nucleotide diversities, supported by Fu and Li's D* neutrality test (1.44055; P < 0.05). The mtDNA control region sequences of extant pigs in the Lanyu Islet, however, showed high haplotype and nucleotide diversity, and clustered with exotic pigs. These results indicate no maternal lineage mtDNA gene introgression from Formosan wild pigs and introduced exotic pigs to conserved Type I Lanyu pigs, and a severe loss of heterozygosity of mtDNA in conserved Lanyu pigs. The remaining extant pigs on the Lanyu Islet have been introgressed with exotic breeds. Strategies for future conservation of native Lanyu pigs are now even more urgent and important.

Key Words: control region, cytochrome b, genetic diversity, Lanyu pig, mitrochondrial DNA, phylogenetic relationship

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