The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

Abstract

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.

Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe

“…We applied PCA at three resolution levels: using all SNPs, using only bitter receptor SNPs, and using only non-synonymous mutations in bitter receptor genes. Both the PCA and STRUCTURE analyses (Figure 3 ) show a separation between Asian and local European breeds (Iberian) as is typically observed in mtDNA and at the autosomal level [ 23 , 24 ]. Remarkably, we observed a continuum rather than a clear geographic split between Asia and Europe.…”

Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids

“…After the first divergence between European and Asia wild boars, pigs were domesticated independently across Eurasia with rare transcontinental genetic interchanges in the early ages. Subsequent divergence occured across two subgroups (European and Asian types) 18 19 . In recent centuries, pigs were raised under various artificial selection practices in different geographical regions.…”

Single nucleotide markers of D-loop for identification of Indian wild pig (Sus scrofa cristatus)

“…These samples were screened and confirmed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, which has been reported in our recent study for differentiation of Indian wild pig from exotic and local domestic pigs [ 2 ]. DNA was subjected to routine PCR amplification by using universal primers for D-loop region (Forward- 5’-AGG AGACTAACTCCGCCAT-3’, Reverse-5’- CGCGGATACTTGCATCTGT3’) [ 5 ] in a gradient thermal cycler (Eppendorf, India) in a final volume of 50 µl containing 40-50 ng of extracted DNA, 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl 2 , 0.2 mM of each dNTP, 1 unit of Taq polymerase (Applied Biosystems), 0.5 µg/µl bovine serum albumin, and 20 pmol of each primer. The amplification parameters were 94°C for 15 min followed by 35 cycles of 94°C for 30 s, 60°C for 45 s, and 72°C for 1 min with final extension at 72°C for 10 min prior to a 4°C hold.…”