Interpopulation and intrapopulation maternal lineage genetics of the Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences1

Abstract

The Lanyu pig is an indigenous breed from the Lanyu Islet, which is 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. Entire mitochondrial genomes of both types of Lanyu pig comprised 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes. Only 2 haplotypes of the mitochondrial DNA (mtDNA) 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 the control region from Asian and European type breeds, Formosan wild pigs, and exotic breeds. Significant loss of genetic diversity of mtDNA 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 mtD-NA 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.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

“…It is genetically separated from its European cousins and other Asian breeds by quite some distance (Wu et al, 2007; Jiang et al, 2008; Chang et al, 2009). Based on coat color and its original habitat (Lanyu [Orchid] Islet), the Lanyu pig is generally assigned as a domesticated Asian pig breed.…”

“…The Lee-Sung miniature pig breed was generated by crossing Lanyu (NTU) with Landrace and back to Lanyu (NTU) (Wu et al, 2009). It has been documented that the Lanyu breed possesses a remote genetic relationship with Asian and European type commercial breeds (Jiang et al, 2008; Chang et al, 2009). However, further assessment of genetic distance, genetic diversity, and differentiation among close lineage breeds (Spotty Lanyu and Binlang Lanyu pig) and related synthetic breeds (Mitsai Lanyu and Lee-Sung pig) remains incomplete.…”

Phylogenetic relationships of pig breeds from Shandong province of China and their influence by modern commercial breeds by analysis of mitochondrial DNA sequences

“…Comparison of Cytb and CR as phylogenetic markers to investigate genetic relationships of pig breeds Both the mtDNA Cytb and CR DNA sequences are widely used as phylogenetic markers in molecular systematics (Ghivizzani et al, 1993;Alves et al, 2003;Clop et al, 2004;Fang and Andersson, 2006;Wu et al, 2007;Jiang et al, 2008). However, compared with Cytb, CR has a larger sequence variation, and is useful to compare the genetic diversity in the study.…”

“…So far, the phylogenetic relationships of Chinese indigenous pig breeds has been evaluated by microsatellite markers (Fan et al, 2002;Yang et al, 2003;Zhang et al, 2003;Li et al, 2004;Fang et al, 2005;Megens et al, 2008) and mitochondrial DNA (mtDNA) sequence Fang and Andersson, 2006;Wu et al, 2007;Jiang et al, 2008). However, the vast genetic resources in China are still poorly characterized, except a few very famous breeds.…”

Genetic differentiation between Cinta Senese and commercial pig breeds using microsatellite

“…Recently, the phylogenetic relationships among eight pig breeds from Shandong province of China and to what extent they were affected by the modern commercial breeds (Duroc, Yorkshire and Landrace) were determined in maternal lineage by using direct sequencing of mitochondrial Cytb and partial control region (CR) DNA sequence (Wang et al 2010), two molecular markers widely used to analyze the phylogenetic relationships of closely related groups (Jiang et al 2008). …”