BackgroundPigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.ResultsA deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.ConclusionsKey events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation. Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0345-y) contains supplementary material, which is available to authorized users.

Heat shock proteins act as molecular chaperones that have preferentially been transcribed in response to severe perturbations of the cellular homeostasis such as heat stress. Here the traits respiration rate (RR), rectal temperature (RT), pack cell volume (PCV) and the individual heat tolerance coefficient (HTC) were recorded as physiological responses on heat stress (environmental temperatures) in Bos taurus (crossbred Holstein Friesian; HF) and B. indicus (Thai native cattle: White Lamphun; WL and Mountain cattle; MT) animals (n = 47) in Thailand. Polymorphisms of the heat shock protein 90-kDa beta gene (HSP90AB1) were evaluated by comparative sequencing. Nine single nucleotide polymorphisms (SNP) were identified, i.e. three in exons 10 and 11, five in introns 8, 9, 10 and 11, and one in the 3′UTR. The exon 11 SNP g.5082C>T led to a missense mutation (alanine to valine). During the period of extreme heat (in the afternoon) RR and RT were elevated in each of the three breeds, whereas the PCV decreased. Mountain cattle and White Lamphun heifers recorded significantly better physiologic parameters (p < 0.05) in all traits considered, including or particularly HTC than Holstein Friesian heifers. The association analysis revealed that the T allele at SNP g.4338T>C within intron 3 improved the heat tolerance (p < 0.05). Allele T was exclusively found in White Lamphun animals and to 84% in Mountain cattle. Holstein Friesian heifers revealed an allele frequency of only 18%. Polymorphisms within HSP90AB1 were not causative for the physiological responses; however, we propose that they should at least be used as genetic markers to select appropriate breeds for hot climates.

The mtDNA control region of 72 Thai native pigs and 11 Thai wild boars indigenous to Northern Thailand was comparatively sequenced. In total, 36 nucleotide variations that accounted for 24 haplotypes have been described (TNH01 to TNH20 and TWH01 to TWH04). These haplotypes and further publicly available mtDNA haplotypes were used to assess phylogenetic relationships. Twenty-three of the 24 haplotypes became integrated into the Asian clade of the phylogenetic tree and eight of them recapitulated another major cluster of haplotypes within this clade (Thai haplogroup, THG). Only haplotype TNH01 fit in with the European clade of the phylogenetic tree. An additional analysis using 510 bp of the mtDNA incorporated the THG haplotypes in to clade MTSEA (mountainous and Southeast Asian distribution) to form haplogroup MTSEA-THG. Recently, MTSEA was renamed in MC3. MC3 contains only signatures of pigs scattered across the Indo-Burma Biodiversity Hotspot (IBBH), a region including Thailand to the Kra Isthmus. Here we propose a putative independent porcine domestication event in South-east Asia (SEA). All haplotypes of haplogroup MTSEA-THG have revealed unique and previously unknown nucleotide signatures at positions 24 (nucleotide A) and at positions 183 (nucleotide C) that differentiate them from all other porcine mtDNA haplotypes.

Objective European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results The results showed that Thai pig populations had a high genetic diversity with mean total and effective (N e ) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity (H e ) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher H e compared to observed heterozygosity (H o ) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei’s genetic distance, mean F ST estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

We have isolated and characterized the porcine testis-specific phosphoglycerate kinase 2 (PGK2) gene, and 1665 bp of full-length PGK2 cDNA were also compiled using modified rapid amplification 5'-RACE and 3'-RACE information. The results of genomic and cDNA sequences of the porcine PGK2 gene demonstrated that it is a single-exon intronless gene with a complete open reading frame of 1251 bp encoding a PGK protein of 417 amino acids. Real-time quantitative PCR results showed that PGK2 mRNA was solely expressed in the testis. There was a lower amount of PGK2 expression in the testis of a 10-month-old herniated boar and a very small amount of PGK2 expression in the testis of an 8-week-old cryptorchid piglet compared to an adult boar. Two SNPs in the PGK2 gene (SNP-A: T427C; SNP-B: C914A) resulting in amino acid substitutions (SNP-A: Ser102-Pro102; SNP-B: Thr264-Lys264) were detected and genotyped among six pig breeds. The nucleotide C at SNP-A responsible for the amino acid exchange to proline could lead to the loss of a casein kinase II (CK2) phosphorylation site in the PGK2 peptide. Association analyses between PGK2 genotypes and several traits of sperm quantity and quality were performed. The results showed that SNP-B has a positive significant effect on semen volume in the breed Pietrain (p = 0.08), i.e., boars carrying genotype CC revealed an increased volume of 49 ml compared with boars having the genotype AA.