Foreign Pig Breeds Research Articles

Potential selection for lipid kinase activity and spermatogenesis in Henan native pig breeds and growth shaping by introgression of European genes

BackgroundChina has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds.ResultsWe found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33–40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups.ConclusionsAdmixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses.

Genome-wide detection of CNV regions between Anqing six-end-white and Duroc pigs

BackgroundAnqing six-end-white pig is a native breed in Anhui Province. The pigs have the disadvantages of a slow growth rate, low proportion of lean meat, and thick back fat, but feature the advantages of strong stress resistance and excellent meat quality. Duroc pig is an introduced pig breed with a fast growth rate and high proportion of lean meat. With the latter breed featuring superior growth characteristics but inferior meat quality traits, the underlying molecular mechanism that causes these phenotypic differences between Chinese and foreign pigs is still unclear.ResultsIn this study, copy number variation (CNV) detection was performed using the re-sequencing data of Anqing Six-end-white pigs and Duroc pigs, A total of 65,701 CNVs were obtained. After merging the CNVs with overlapping genomic positions, 881 CNV regions (CNVRs) were obtained. Based on the obtained CNVR information combined with their positions on the 18 chromosomes, a whole-genome map of the pig CNVs was drawn. GO analysis of the genes in the CNVRs showed that they were primarily involved in the cellular processes of proliferation, differentiation, and adhesion, and primarily involved in the biological processes of fat metabolism, reproductive traits, and immune processes.ConclusionThe difference analysis of the CNVs between the Chinese and foreign pig breeds showed that the CNV of the Anqing six-end-white pig genome was higher than that of the introduced pig breed Duroc. Six genes related to fat metabolism, reproductive performance, and stress resistance were found in genome-wide CNVRs (DPF3, LEPR, MAP2K6, PPARA, TRAF6, NLRP4).

The complete mitochondrial genome of Min pig (Hebao) and a phylogenetic analysis

The complete mitochondrial genomes of Min pig (Hebao) are published in this paper. The full length of mtDNA is 16,719 bp and contained 13 PCGs, 2 rRNA and 22 tRNA, and 1D-loop(MN258706). A phylogenetic tree with the 13 protein-coding genes sequences of Min pig (Hebao) together with 45 other Chinese pig breeds and 7 foreign pig breeds was constructed. The results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes. The result of phylogenetic analysis showed that the genetic relationship of Min pig (Hebao) is closer to that of Dapulian pigs.

An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis.

Streptococcus suis is a zoonotic swine pathogen and a major public health concern in Asia, where it emerged as an important cause of bacterial meningitis in adults. While associated with food-borne transmission in Asia, zoonotic S. suis infections are mainly occupational hazards elsewhere. To identify genomic differences that can explain zoonotic potential, we compared whole genomes of 98 S. suis isolates from human patients and pigs with invasive disease in the Netherlands, and validated our observations with 18 complete and publicly available sequences. Zoonotic isolates have smaller genomes than non-zoonotic isolates, but contain more virulence factors. We identified a zoonotic S. suis clone that diverged from a non-zoonotic clone by means of gene loss, a capsule switch, and acquisition of a two-component signalling system in the late 19th century, when foreign pig breeds were introduced. Our results indicate that zoonotic potential of S. suis results from gene loss, recombination and horizontal gene transfer events.

Molecular microevolution and epigenetic patterns of the long non-coding gene H19 show its potential function in pig domestication and breed divergence.

BackgroundThe domestic pig Sus scrofa domesticus originated from the wild boar S. scrofa about 10,000 years ago. During domestication, drastic morphological, physiological, and behavioral changes developed between domestic pigs and wild boars through artificial and natural selection. The long non-coding RNA (lncRNA) H19, which is located within the imprinting gene cluster H19-IGF2, plays an important role in regulating muscle development in humans and mice. This study systematically analyzed the molecular evolution of H19 and its possible epigenetic changes during pig domestication and breeding to explore the genetic and epigenetic contributions of H19 to pig domestication.ResultsThe molecular evolution of H19 was initially analyzed on a large phylogenetic scale. Results showed that the gene was highly conserved within a broad range, especially in the 5′ terminal sequence. The molecular evolution of the gene was then analyzed using published re-sequencing data of 30 wild boars from Tibet, 3 wild boars from Sichuan, and 15 native pigs from other regions in China. Eight polymorphic sites were identified, and the nucleotide diversity (π) value within the H19 gene body was significantly higher (Z-test, P < 0.05) in domesticated pigs than in wild pigs. However, no significant divergence occurred between domesticated and wild pigs. Single nucleotide polymorphisms in the 3′ terminal sequence were surveyed in other Chinese local breeds and foreign pig breeds. We observed a consistently higher diversity in domesticated pigs than in wild pigs. The methylation pattern of the H19 gene in pigs was subsequently analyzed using published methylated DNA immunoprecipitation data and an unpublished single-base resolution liver methylome. Analysis results showed distinct methylation levels in some tissues. Among the samples surveyed, Landrace showed the lowest methylation level, followed by the Guizhou wild boar, whereas the Enshi pig exhibited the highest methylation level in the 2 kb upstream region of the H19 gene. Liver transcriptome data suggested that Landrace harbored the highest expression of the H19 gene, followed by the Guizhou wild boar, whereas the Enshi pig harbored the lowest expression of the gene. Differential methylation sites (DMSs) among the three breeds were mainly identified in the 2 kb upstream region of the H19 gene. In the Enshi pig, we detected allele-specific methylation (ASM) regions in the 2 kb upstream region of the H19 gene. Most of the DMSs in the upstream 2 kb region of the gene were also located in the ASM region in this breed.ConclusionsMolecular analyses suggest that the H19 gene was highly conserved during large-scale evolution and exhibited genotype differentiation during domestication and breed differentiation. The drastic diversity pattern between domestic and wild pigs in the H19 gene body, which was highly conserved during large-scale evolution, suggests that this gene might have played roles in the breed differentiation of domestic pigs. Methylation analysis indicates an opposite epigenetic regulation direction between Chinese and European pig (EU) domestication, which resulted in opposite expression changes in this gene between the two domesticated groups. Our preliminary analyses on DMSs among different pig breeds and ASM imply that imprinting was associated with methylation differences. This study systematically demonstrates the genetic and epigenetic patterns of H19 during pig domestication and provide valuable cues and basis for further research on the function of H19 in pig domestication.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0657-5) contains supplementary material, which is available to authorized users.

Influence of crossing Polish and foreign pig breeds on physicochemical traits of longissimus lumborum muscle

The aim of this study was an assessment of physicochemical traits characterizing the longissimus lumborum muscle in fatteners originating from an application of various variants of commodity crossbreeding with a contribution of 2 Polish and 2 foreign breeds. The research material was collected from the right half-carcass from 180 crossbred fatteners selected randomly from a technological group (60 heads in each), with a division of gilts and hogs. The meat was subjected to laboratory examinations according to the procedures and requirements of the Association of Official Agricultural Chemists International. Pig breeds used in the crossbreeding affected the values of the examined physicochemical traits significantly from a culinary and technological point of view. Crossbred fatteners from the backcrossing, compared to 4-breed single crossing, were characterized by statistically significantly higher dry matter content in the longissimus lumborum muscle and higher water-holding capacity. In terms of fat and collagen content in the muscle, the crossbred fatteners from the backcrossing demonstrated poorer parameters compared to 4-breed crossbreds. Statistically significant differences in the range of muscle color determinants were noted between the groups of fatteners. The most profitable parameters were observed in crossbred fatteners ¾ PLW ¼ PL and ¾ PL ¼ PLW.

Performance traits in different generations of imported Danish Landrace pigs

Abstract. The number of foreign pig breeds imported to Lithuania has increased, especially Landraces. Animals imported from other countries get into different environmental conditions. Decisions about adaptation of Danish Landraces were made when analysing the changes in the data for productivity of imported pigs and their offsprings of F1-F6 generations born in Lithuania. The work was carried out in the years 1998–2006. Because of adaptation to new environmental conditions, litter size, litter weight of piglets at 21 days of age and survival rate percent of piglets for primaparous sows of Danish Landrace breed, born and grown in Lithuania, was improving, in comparison with imported primaparous sows. According to evaluation data analysis of the control fattening and carcass for Danish Landrace progeny born in the country, offspring of sixth generation (F6) distinguished by the best fattening performance. However, tendency manifested, that with increasing daily gain in many cases meatiness traits of pigs are getting worse. Muscularity of F6 Landraces was 1.7–2.9 % lower than of F2-F5 progeny of this breed (P&lt;0.05–0.01). Therefore, when striving in the adaptation process to stabilise specific traits of Landrace pigs, especially fattening performance and meatiness, besides balanced feeding and making of good keeping conditions, it is also purposeful regularly to import boars (each 3–4 years) of this breed into breeding centres or to use Al stations services.

Isolation of new alleles of the swine &lt;I&gt;TLR4&lt;/I&gt; gene and analysis of its genetic variation

Using the PCR-SSCP method, the genetic variation in exon 1 of the TLR4 gene was detected among 893 animals, including Asian wild boars, 3 imported commercial and 10 Chinese indigenous swine breeds. This was conducted to analyze the polymorphisms of exon 1 of TLR4 gene in native and foreign pig breeds and aimed at providing a theoretical foundation for further research on the role that TLR4 gene played in immune and defense system. New alleles were isolated for exon 1 of the swine TLR4 gene for the first time, There were 6 genotypes and 3 alleles, in which the Duroc appeared AA, BB, CC, AB, AC and BC genotypes; Sutai pig, which has Duroc pig origin, were detected to be BB, CC, and BC genotypes; Yorkshire and Landrace were detected to be CC and BC genotypes. Wild boar and all 10 Chinese native pig breeds appeared highly conserved in exon 1 of TLR4 gene, with only CC genotype. Among the 3 homozygous genotypes, the CC genotype matches the sequence in GenBank, while a G93C synonymous mutation and a G194A nonsense mutation were found in the BB and AA genotypes, respectively. The correlation between these two mutation points of TLR4 gene with resistance to stress and disease is worthy of further study.

Genetic variants of BMP15 and BMPR- IB genes and association with litter size in pig

Four hundred and eighty-one pigs including Laiwu Black,Lulai Black,Licha Black,Luyan White,New Yimeng Black,Yorkshire,Landrace and Duroc were selected to detect genetic variants of BMP15 and BMPR-IB genes by PCR-SSCP.The genetic effects of the two genes on litter size were analyzed by least squares method.The results showed that the polymorphic sites of both BMP15 and BMPR-IB genes were found in all populations tested.The genotype distribution,however,revealed great differences between Shandong local breeds and foreign pig breeds.The effects of genotypes on total number born(TNB) and number born alive(NBA) were significant(P0.05).For BMP15 gene,in AA genotypic sows,the average TNB and NBA of foreign pig breeds were 1.20 and 1.64 more than that of Shandong local breeds,respectively(P0.05);in CC genotypic sows,the average TNB and NBA of foreign pig breeds were 1.20 and 0.82 more than that of Shandong local breeds,respectively(P0.05).For BMPR-IB gene,in Shandong local breeds,the average TNB and NBA of AA were 0.49 and 0.51 more than that of BB,respectively(P0.05);while the average TNB and NBA of BB was 1.05 and 0.90 more than that of AA in the foreign pig breeds,respectively(P0.05).

Molecular Characterization, Mapping, and Haplotype Analysis of Porcine Matrix Metalloproteinase Genes MMP1 and MMP10

Matrix metalloproteinases (MMPs) are a family of enzymes that cleave protein components of the extracellular matrix, such as collagens, laminin, fibronectin, and proteoglycans, playing a role in degradation of the matrix of the uterus and in embryo implantation. We report the identification of two members of the MMP gene family in swine. The porcine MMP1 and MMP10 genes comprise 10 exons and 9 introns spanning approximately 8,460 and 7,030 bp. Of 28 potential single nucleotide polymorphisms found in the genomic region, five polymorphic positions were analyzed using PCR-RFLP. Allelic frequencies and haplotypes were analyzed in five pig breeds (n = 280). The AC haplotype of MMP1 and ATG haplotype of MMP10 were not detected in two foreign pig breeds. Association analysis in a French Large White population (n = 164, total four traits) showed no association between haplotypes and reproduction performance. In addition, porcine MMP1 and MMP10 were mapped on SSC9p(13) and SSC2q(21), respectively, in agreement with comparative mapping data.

Relationship of genetic polymorphism of &lt;I&gt;PRLR&lt;/I&gt; and &lt;I&gt;RBP4&lt;/I&gt; genes with litter size traits in pig

The polymorphism of prolactin receptor (PRLR) and retinol-binding protein 4 (RBP4) genes was detected by PCR-RFLP method, and the effects of PRLR and RBP4 genes on litter size traits in pig were analyzed by the least square analysis. Data of total number born (TNB) and number born alive (NBA) from 323 sows, including five Shandong local pig breeds and three foreign pig breeds, were collected. The results showed that the polymorphic sites of both PRLR and RBP4 genes were found in all populations tested. The genotype distribution, however, revealed great differences between Shandong local pig breeds and foreign pig breeds. The effects of genotypes on TNB and NBA were significant (P<0.05). The homozygote AA was the most prolific genotype. For PRLR gene, AA genotypic sows of Shandong local pig breeds and foreign pig breeds produced 1.03 TNB, 0.89 NBA, and 1.26 TNB, 1.11 NBA more than BB genotypic sows, respectively. For RBP4 gene, AA genotypic sows of Shandong local pig breeds and foreign pig breeds produced 0.59 TNB, 0.51 NBA and 0.72 TNB, 0.64 NBA more than BB genotypic sows, respectively.

Analysis of polymorphisms in exon 14 in porcine Mx1 gene and identification of new mutation points

By the PCR-RFLP method, the polymorphisms of exon 14 of Mx1 gene were detected in 7 native and foreign pig breeds. Taken together with the analysis of restriction enzyme Hin6 I digestion, there were 6 genotypes and 3 alleles. And, all individuals of Duroc exhibited the AA genotype but the Sutai pigs exhibited all three kinds of genotypes. The BB genotype was detected only in Meishan pigs and their derivate Sutai pigs. Among all pig breeds, the allele B only appeared in Chinese indigenous pig breeds and developed pig breed in this study, and the allele A was dominant allele in all pig breeds except for Songliao black pig. The results of Chi Square test showed that there were abundant polymorphisms in all pig breeds. The gene frequency of Meishan pig and Songliao black pig showed greatly significant difference to other pig breeds (P<0.01), Sutai pig showed greatly significant difference (P<0.01) to other pig breeds except for Pietrain; and Huai pig showed greatly significant differences (P<0.01) with Pietrain and other indigenous Chinese pig breeds, but no difference with Duroc and Yorkshire (P>0.05). Three new mutation points in three genotypes were identified by sequencing comparison analysis of PCR products, two of which resulted in Thr-->Ala and Glu-->Arg respectively, the last one was a silence mutation, the Glu-->Arg mutation point and this silence mutation point only appeared in the individuals with the BB genotype.

Genetic Variation of Exon 2 of SLA-DQB Gene In Chinese Pigs

A 273 base pair (bp) fragment of the SLA-DQB gene including parts of intron 1 and exon 2 has been investigated using PCR-RFLP in 38 indigenous Chinese pig breeds, two Chinese wild boars, and three foreign pig breeds. The restriction enzyme RsaI revealed three polymorphic sites in the 273 bp fragment for the pig breeds studied. In total, four alleles resulting in 10 genotypes were found. Twenty pig breeds are not in Hardy-Weinberg equilibrium at this locus. The allele frequency of a chi-square test showed that there is significant difference (P < 0.05) among six Chinese pig groups, and an even greater significant difference (P < 0.01) was found between Chinese and European pig breeds.

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.