The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.     

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.     

6个中国猪地方品种和3个瑞典猪DNA分子系统发育相关关系

线粒体DNA遗传多样性用于评价6个中国地方猪种和3个瑞典家猪系统发育关系。采用PCR和序列分析方法得到了来自9个品种140头猪的线粒体中控制区440bp和细胞色素b基因798bp核苷酸序列。系统发育分析结果表明：6个中国地方猪种起源于亚洲野猪。中国地方猪种和欧洲野猪的线粒体DNA核苷酸序列变异发生在413000－875000年以前,而亚洲紧猪的变异仅发生在7000－156000上以前,由于2000年以前或18世纪初中国猪种导入欧洲家猪,因此瑞典家猪既属于欧洲类也属于亚洲类。     

Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable?

The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.     

猪a1-岩藻糖转移酶基因(FUT1)M857位点遗传变异分析

肠毒素大肠杆菌 (ETEC) F18是引起仔猪断奶后水肿和腹泻病的主要病原菌, a-1岩藻糖转移酶(FUT1)基因是ECEC F18侵染猪小肠的受体蛋白基因。利用PCR-RFLP方法检测了1个野猪以及20个中外家猪猪种(群)共696个个体在FUT1基因开放阅读框架的857核苷酸位点的遗传变异, 结果表明: 在所有猪种中, 均未检测到抗性的AA型纯合子, 在外来猪种杜洛克和约克夏、国内猪种临高猪和杂交猪种中检测到AG型杂合子, 外来猪种中的皮特兰、长白猪以及除临高猪外的所有国内猪种和野猪均表现为极端的单态分布, 只有易感的GG基因型。研究结果提示, 中国地方猪种不具备抵抗ETEC F18大肠杆菌的遗传基础, 与外来猪种确实存在差异, 这种差异可能与各自不同的起源有关, ETEC F18抗性基因可能起源于欧洲野猪; 并推测猪种的生长速度与ETEC F18大肠杆菌病的发生具有密切的关系。     

The origin of the domestic pig: independent domestication and subsequent introgression

The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before domestication approximately 9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.     

Genetic polymorphism of erythrocyte esterase-D in pigs

The erythrocyte esterase-D (Es-D) of four European-American pig breeds, two Taiwan native pigs (Taoyuan and Short ear breeds), Philippine native pig and wild boar populations (Sus scrofa riukiuanus) in Japan was investigated by using starch gel electrophoresis. Analysis of parentage records of the pigs revealed that the phenotypic variation of erythrocyte esterase-D was controlled by two codomi-nant alleles Es-D^A and Es-D^B. The allele Es-D^b was mostly found in three European -American pig breeds, Landrace (0.100), Hampshire (0.135) and Duroc (0.102). All of the wild boar populations were monomorphic for allele Es-D^A.     

Immunogenetic characteristics of the gene fund of Kakhetian swine and dynamics of population parameters in several generations

Some peculiarities of gene fund and dynamics of populational characters of the oldest in Europe Kakhetian (Georgian) pigs were investigated during 18 years (10 generations). Genetic peculiarity of the aboriginal species populations in conditions of intensive pressure of natural selection and relatively weak artificial selection was determined with the help of codominant alleles of the blood groups E system. Considerable qualitative and quantitative differences were detected between Kakhetian pigs and all subspecies of European boars and domestic pigs of cultured breeds studied. Kakhetian pigs are strongly similar to wild boar, as concerns their morpho-physiological and behavioral characteristics. However, the assumption that they originated from Romanian (Caucasian) wild boar by direct domestication, without hybridization, is wrong, since they have alleles which are never found in European wild boars. The results of comparative study of Kakhetian and other domesticated and wild pig forms characteristics makes it possible to suppose that the presence in Kakhetian pigs gene fund of some alleles of East Asian origin is due to a certain participation of the Large White and Mangalica breeds in their phylogenesis. The two latter breeds, in their turn, obtained these alleles as a result of two waves of pig importation in Europe from the South-East Asia (on the eve of a.d. and about 150-200 years ago). This is indirectly confirmed by historical and zootechnical data.     

野猪及其与家猪杂种猪Myostatin基因3'编码区的克隆和序列分析

Myostatin, which is a highly conservative gene among breeds, is a negative regulator of muscle. The 3' coding region of wild boar and crossbred pig myostatin was cloned by RT - PCR and sequenced. Compared with that of GenBank, the homology of the nucleotide sequence between wild bear and crossbred pig is identical in this region indicating that domestic pigs were evolved from wild boar and there was not changed in this region during the evolution processes.     

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.     

The development of the gene pool in the microevolution of Sus scrofa and the role of heterozygosity in the breed-forming process

The gene pool formation of the modem domestic breeds of pig Sus scrofa domestica and their genesis based on hybridization of wild ancestral forms of the European and Asian origin were studied using molecular immunogenetic methods. Males of the European and Central Asian S. scrofa subspecies (S. s. scrofa and S. s. nigripes were hybridized with domestic pigs of the Swedish Landrace and Vietnamese Black Masked breeds. In addition, we examined the genotypic structure of 65 wild, aboriginal, and local populations as well as cultured breeds, including the stock breeds with different levels of selection. Frequencies of alleles and suballelles of the chromosome 4 locus controlling antigens of the L blood group system were analyzed. The origin of marker suballeles of the European and Asian origin was estimated in the most widespread world pig breeds. Unexpectedly, a strikingly high frequency of the Asian elements was found in the most productive European and American breeds, as well as in the best breeds of Russia and other CIS countries. Only one form of heterozygosity (bcgi/bdfi) was found in a population of wild European ancestors, whereas domestic pig breeds displayed heterozygosity for far more numerous suballeles of the locus studied. Animals heterozygous for alleles of the European and Asian origin showed higher adaptivity and fertility.     

Genome data from a sixteenth century pig illuminate modern breed relationships

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.     

Numerical variation of nucleolar organizer regions after silver staining in domestic and wild Suidae (Mammalia)

Selective silver staining was used to investigate the cellular distribution of numbers of nucleolar organizer regions (NORs) in domestic pigs (Sus scrofa) of eight different breeds, the European wild boar (S. scrofa scrofa), Indonesian wild boar (S. scrofa vittatus), Javan warty pig (S. verrucosus), Sulawesi warty pig (S. celebensis), and pigmy hog (S. salvanius). In the domestic pig as well as in the wild (sub)species of Sus, actively transcribing ribosomal RNA genes were found to be present in the secondary constrictions of chromosome pairs 10 and 8. Chromosomes 10 were consistently Ag-positive. Chromosomes 8 less frequently showed Ag-NORs, resulting in different mean numbers of Ag-NORs per individual animal. Mean Ag-NOR numbers per breed or (sub)species were generally higher in the wild representatives of Sus than in the domestic breeds. The highest mean numbers of Ag-NORs were observed in the Meishan breed and in S. celebensis and S. salvanius. The Meishan breed appears to be conservative in Ag-NOR staining pattern, being more comparable to the Asian wild Suidae than to the European breeds.     

Evidence of genetic variability for digestive efficiency in the growing pig fed a fibrous diet

Energy digestibility in the growing pig increases with BW increase and may differ between breeds of pigs or between lines selected on criteria other than digestion. However, little is known about the variability in energy digestibility within a line or a breed of pigs, especially when fibrous diets are fed. For this purpose, 20 Large White castrated male growing pigs originating from four boars (five per boar), and three to four sows per boar, were fed a high dietary fibre (DF) diet (18% NDF) and measured over 10 consecutive weeks (30 to 95 kg BW range) for their apparent faecal energy, nitrogen and organic matter digestibility. Each week, faeces were totally collected over 5 days and the feed dry matter intake over the same days was recorded. All digestibility coefficients increased regularly (P < 0.001) over the experimental periods or with BW increase (+0.6 point/10 kg BW increase for energy); this rate of increase was not affected by boar origin (no interaction; P > 0.05). The digestibility coefficients were affected by boar origin (P < 0.005 for energy), with about 2 points for energy between the extremes (81.7% v. 79.5%), and there was no marked interaction between boar origin and period. These preliminary results suggest the possibility of selecting growing pigs for an increased digestive efficiency when fed high DF diets.     

The development of the gene pool in the microevolution of <Emphasis Type="Italic">Sus scrofa</Emphasis> and the role of heterozygosity in the breed-forming process

The gene pool formation of the modern domestic breeds of pig Sus scrofa domestica and their genesis based on hybridization of wild ancestral forms of the European and Asian origin were studied using molecular immunogenetic methods. Males of the European and Central Asian S. scrofa subspecies (S. s. scrofa and S. s. nigripes were hybridized with domestic pigs of the Swedish Landrace and Vietnamese Black Masked breeds. In addition, we examined the genotypic structure of 65 wild, aboriginal, and local populations as well as cultured breeds, including the stock breeds with different levels of selection. Frequencies of alleles and suballelles of the chromosome 4 locus controlling antigens of the L blood group system were analyzed. The origin of marker suballeles of the European and Asian origin was estimated in the most widespread world pig breeds. Unexpectedly, a strikingly high frequency of the Asian elements was found in the most productive European and American breeds, as well as in the best breeds of Russia and other CIS countries. Only one form of heterozygosity (bcgi/bdfi) was found in a population of wild European ancestors, whereas domestic pig breeds displayed heterozygosity for far more numerous suballeles of the locus studied. Animals with heterozygosity for alleles of the European and Asian origin showed higher adaptivity and fertility.__________Translated from Genetika, Vol. 41, No. 4, 2005, pp. 566–576.Original Russian Text Copyright © 2005 by Tikhonov.     

Genetic relationship amongst the major non-coding regions of mitochondrial DNAs in wild boars and several breeds of domesticated pigs

We completed phylogenetic analysis of the major non-coding region of the mitochondrial DNA (mtDNA) from 159 animals of eight Euro-American and six East Asian domesticated pig breeds and 164 Japanese and five European wild boars. A total of 62 mtDNA haplotypes were detected. Alignment of these regions revealed nucleotide variations (including gaps) at 73 positions, including 58 sites with transition nucleotide substitutions, and two transversion substitutions. Phylogenetic analysis of the sequences could not organize domestic pig breeds into discrete clusters. In addition, many of the haplotypes found in members of diverged clustering groups were found primarily in Euro-American pig breeds, indicating extensive introgression of Asian domestic pigs into European breeds. Furthermore, phylogenetic analysis allocated the DNA sequences of non-coding regions into two different groups, and the deepest branchpoint of this porcine phylogeny corresponded to 86 000-136 000 years before present. This time of divergence would predate the historical period when the pig is thought to have been domesticated from the wild boar.     

Metabolomics evidences plasma and serum biomarkers differentiating two heavy pig breeds

In pigs, many production traits are known to vary among breeds or lines. These traits can be considered end phenotypes or external traits as they are the final results of complex biological interactions and processes whose fine biological mechanisms are still largely unknown. This study was designed to compare plasma and serum metabolomic profiles between animals of two heavy pig breeds (12 Italian Large White and 12 Italian Duroc), testing indirectly the hypothesis that different genetic backgrounds might be the determining factors of differences observed on the level of metabolites in the analyzed biofluids between breeds. We used a targeted metabolomic approach based on mass spectrometric detection of about 180 metabolites and applied a statistical validation pipeline to identify differences in the metabolomic profiles of the two heavy pig breeds. Blood samples were collected after jugulation at the slaughterhouse and prepared for metabolomics analysis that was carried out using the Biocrates AbsoluteIDQ p180 Kit, covering five different biochemical classes: glycerophospholipids, amino acids, biogenic amines, hexoses and acylcarnitines. A statistical pipeline that included the selection of the most relevant metabolites differentiating the two breeds by sparse Partial Least Squares Discriminant Analysis (sPLS-DA) was coupled with a stability test and significance test determined with leave one out and permutation procedures. sPLS-DA plots clearly separated the pigs of the two investigated breeds. A few metabolites (a total of five metabolites considering the two biofluids) involved in key metabolic pathways largely contributed to these differences between breeds. In particular, a higher level of the sphingomyelins SM (OH) C14:1 (both in plasma and serum), SM (OH) C16:1 (in serum) and SM C16:0 (in serum) were observed in Italian Duroc than in Italian Large White pigs and the inverse was for the biogenic amine kynurenine (in plasma). The level of another biogenic amine (acetylornithine) was higher in Italian Large White than in Italian Duroc pigs in both analysed biofluids. These results provided biomarkers that could be important to understand the biological differences between these two heavy pig breeds. In particular, according to the functional role played by sphingomyelins in obesity-induced inflammatory responses, it could be possible to speculate that a higher level of sphingomyelins in Italian Duroc might be related to the higher interrmuscular fat deposition of this breed compared with the Italian Large White. Additional studies will be needed to evaluate the relevance of these biomarkers for practical applications in pig breeding and nutrition.     

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high‐density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar‐hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig–wild boar ancestry.     

Linkage disequilibrium decay and haplotype block structure in the pig

Linkage disequilibrium (LD) may reveal much about domestication and breed history. An investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorphisms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending up to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks up to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.     

Inferring the origin and genetic diversity of the introduced wild boar (<Emphasis Type="Italic">Sus scrofa</Emphasis>) populations in Argentina: an approach from mitochondrial markers

The Eurasian wild boar (Sus scrofa Linnaeus, 1758) was introduced into Argentina at the beginning of the twentieth century when individuals from Europe were taken to La Pampa province for hunting purposes. Starting from there, a dispersal process began due to the invasive characteristics of the species and to human-mediated translocations. The main objective of this study was to characterize for the first time, the phylogenetic relationships among wild boars from Argentina with those from Uruguay, Europe, Asia, and the Near East, along with diverse domestic pig breeds in order to corroborate the historical information about the origin of the local populations. To this end, we used mitochondrial Control Region and Cytochrome b sequences from sampled Argentinian wild boars and retrieved from GenBank. The results showed that the majority of the Argentinian wild boar populations descend from European lineages, in particular of the E1 clade, according to the historical records. Remarkably, the population of El Palmar National Park had Asian origin that could be attributed to hybridization with local domestic pigs or to unrecorded translocations. Finally, genetic diversity in Argentinian populations was lower than in Europe and Uruguay meaning that wild boar in Argentina is still under the influence of founder effect and has experienced minor genetic introgression from domestic pigs, representing in this sense a reservoir of the original wild boar genetic variability.