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.     

Introduction of two chromosomal translocations of Sus scrofa nigripes and Sus scrofa scrofa into the genome of Sus scrofa domestica

Summary Hybrids between wild and domestic pigs with two types of translocations in the karyotype were studied. The translocations of type I were first detected in a population of the Middle Asian wild boars. Type II was identified in a populations of the Central European subspecies. A large number of Middle Asian and Central European hybrids and their F₁-F₃ hybrids from crosses with domestic pigs were viable. By means of differential chromosome staining, the mechanism of the formation of synthetic karyotypes, as well as some features of translocation inheritance, were established.The introduction of two translocations into a single genome and the same chromosome set of these hybrids not only modified chromosome number, but also the composition of the linkage groups. The hybrids heterozygous for two translocations and their hybrid progeny are characterized by an obligatory heterozygozity for a large number of genes, gene complexes and linked genes. It is suggested that this heterozygozity may be associated with heterotic events. The use of such hybrids in pig breeding may provide heterosis for viability and productivity.     

Characterization of a polymorphic IGLV gene in pigs (Sus scrofa)

Swine, unlike other artiodactyls, but similar to humans, utilize both lambda and kappa light chain isotypes almost equally in the generation of their antibody repertoire. The porcine antibody light chain loci have previously been characterized in a single Duroc sow in which was seen extensive allelic variation between light chain genes on homologous chromosomes. However, the extent of variation between individuals is completely unknown. Using deep sequencing of cDNA-derived amplicons from five pigs, we report the identification and characterization of an IGLV gene that is functional and highly expressed in some animals, yet completely absent in others. Our findings provide a possible rationale for the known individual-to-individual variation in antibody responses to vaccination, infectious challenge, and subsequent disease outcome.     

The gene map of the pig (Sus scrofa domestica L.): a review.

A review of the present status of the porcine gene map is given with references. A total of 84 loci have now been studied, and genes have been assigned to 17 chromosomes. Among them, six chromosomes are defined by only one marker. No loci have been attributed yet to three chromosomes.     

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Background

The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.

Results

We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels.

Conclusions

We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.     

Cloning,characterization and chromosomal localization of the Sus scrofa SLC31A1 gene

Copper is an essential element necessary for normal function of numerous enzymes in all living organisms. Uptake of copper into the cell is thought to occur through the membrane protein, SLC31A1 (CTR1), which has been described in a variety of species including yeast, human and mouse. In this study, we present cloning, gene structure, chromosomal localization and expression pattern of the Sus scrofa SLC31A1 gene, which encodes a 189 amino acid protein. The (SSC) SLC31A1 gene is organized in four exons and spans an approximately 2.3 kb genomic region. We have localized the gene to chromosome 1q28-q2.13 using a somatic cell hybrid panel. This region shows conservation of synteny with human chromosome 9, where the human SLC31A1 (CTR1) gene has been localized. Expression studies suggest that SLC31A1 mRNA is transcribed in all tissues examined.     

The Complete Mitochondrial DNA Sequence of the Pig (Sus scrofa)

The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present. Received: 2 December 1997 / Accepted: 20 February 1998     

Comparative cytogenetic studies in Sus verrucosus,Sus celebensis and Sus scrofa vittatus (Suidae,Mammalia)

Chromosome studies on the Javan warty pig (Sus verrucosus), the Sulawesi warty pig (S. celebensis) and a subspecies of the wild boar, S. scrofa vittatus, have revealed diploid chromosome numbers of 38. The morphology and C-band size of chromosome 10 are different in S. verrucosus and the two other species. Both S. verrucosus and S. celebensis have a Y chromosome that is larger than the Y chromosome of domestic and wild S. scrofa, and is submetacentric rather than metacentric. There are differences between all three species in the G-banding pattern of the long arm of the Y chromosome. The presence of 2n=38 chromosomes in the Javan warty pig and the Sulawesi warty pig provides new strong evidence that the basic chromosome number in the genus Sus is 38. The differences in karyotype between these pigs (chromosome 10 and the Y chromosome) confirm that they are separate species.     

Genetic diversity in wild (Sus scrofa scrofa) and domestic (Sus scrofa domestica) pigs and their hybrids based on polymorphism of a fragment of the D-loop region in the mitochondrial DNA

We examined the variation in mitochondrial DNA by sequencing the D-loop region in wild and domestic (large-white breed) pigs, in hybrids between domestic and wild pigs, and in Monteiro pigs. A D-loop fragment of approximately 330 bp was amplified by PCR. Sequencing of DNA amplicons identified haplotypes previously described as European and Asian types. Monteiro pigs and wild pigs had European haplotypes and domestic pigs had both European and Asian haplotypes.     

The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (16.5 Morgans) than the genetic map of the homogametic sex (female) (21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.     

Impacts and management of wild pigs Sus scrofa in Australia

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The increased population of the Wild Boar (Sus scrofa L.) in Europe

In this paper the recent population changes of the Wild Boar in different European countries is analysed through the study of hunting statistics. A simultaneous increase in numbers is observed throughout the whole area during the period 1965–1975. From 1975 onwards the population stabilizes itself apart from in peripheral areas like Finland. Potentially favourable factors which play a part in this process are discussed and certain reproductive and dispersive characteristics which favour its invasive behaviour are discussed.     

Annotation of hypothetical proteins orthologous in Pongo abelii and Sus scrofa

A hypothetical protein is predicted to be expressed from an open reading frame without known experimental evidence of translation. They constitute a substantial fraction of proteomes. Domain extraction from these hypothetical sequences helps to search for protein coding genes for protein structural and functional annotation. We describe the analysis of prediction data in a sequence dataset of hypothetical protein orthologs of Pongo abelii (orangutan) and Sus scrofa (pig). It should be noted that these orangutan-pig orthologs are also non-homologous to human proteins. These predicted data find application in the genome wide annotation of proteins in poorly understood genomes.

Abbreviations

PDB - Protein Data Bank, DEG - Database of Essential Genes, CDD - Conserved Domain Database, IUCN - International Union for Conservation of Nature.     

Testis morphometry, duration of spermatogenesis, and spermatogenic efficiency in the wild boar (Sus scrofa scrofa)

The wild boar is a natural inhabitant of Europe, Asia, and North Africa and is phylogenetically the ancestor of the domestic pig. Because of its phylogenetic and economic importance, this species is an interesting model for studying testis function in boars. Therefore, the present study was performed to investigate the testis structure, spermatogenic cycle length, and Sertoli cell (SC) and spermatogenic efficiencies in eight adult wild boars. Each spermatogenic cycle lasted 9.05 days, and the total duration of spermatogenesis was estimated as lasting approximately 41 days. The percentages of testis volume occupied by seminiferous tubules and by Leydig cells were 87% and 6%, respectively. The mean number of SCs per gram of testis was 42 million. The SC (round spermatids per SC) and spermatogenic (daily sperm production per gram of testis) efficiencies were 6.6 cells and 28.6 million, respectively. In general, the testis structure, overall germ cell associations at the different stages of the seminiferous epithelium cycle, and duration of spermatogenesis in the wild boar were similar to those in domestic pigs. Probably because of the small size of Leydig cells (400 microm3), their number per gram of testis (157 million) was the highest among investigated mammalian species. Although the SC efficiency in wild boars was low, their spermatogenic efficiency was comparable to that observed in domestic pigs, mainly because of the higher number of SCs per gram of testis in wild boars. These data suggest that SCs became more efficient during evolution, genetic selection, and domestication in pigs.     

Load transmission in the nasofrontal suture of the pig, Sus scrofa

The nasofrontal suture links the nasal complex with the braincase and is subject to compressive strain during mastication and (theoretically) tensile strain during growth of nasal soft tissues. The suture's ability to transmit compressive and tensile loads therefore affects both cranioskeletal stress distribution and growth. This study investigated the in vitro viscoelastic and failure properties of the nasofrontal suture in the pig, Sus scrofa. Suture specimens from two ages were tested in compression and tension and at fast and slow rates. In additional specimens, strain gauges were applied to the suture and nasal bone for strain measurement during testing. Relaxation testing demonstrated higher elastic moduli in tension than compression, regardless of test rate or pig age. In contrast, maximum elastic moduli from failure tests, as well as peak stresses, were significantly higher in compression than in tension. Sutures from older pigs tended to have higher elastic moduli and peak stresses, significantly so for tensile relaxation moduli. Strain gauge results showed that deformation at the suture was much greater than that of the nasal bone. These data demonstrate the viscoelasticity and deformability of the nasofrontal sutural ligament. The suture achieved maximal resistance to tensile deformation at low loads, corresponding with the low tensile loads likely to occur during growth of nasal soft tissues. In contrast, the maximal stiffness in compression at high loads indicates that the suture functions with a substantial safety factor during mastication.     

The estrous cycle and induction of estrus in the australian feral sow (Sus scrofa)

In the first of 2 experiments, the estrous cycles of 11 Australian feral sows were studied. In 9 of the 11 sows the cycle was characterized by cyclic occurrences of low (0 to 2 ng/ml) and high (24.2 to 47.2 ng/ml) levels of progesterone. The low levels were associated, in all sows but one, with the standing response, lasting from 1 to 4 days, to a feral boar. Concomitant cyclic changes in vulval swelling and consistency of the vaginal mucus were also observed. Using intervals between the standing estrous response or the marked changes in the secretion of progesterone, the mean length of the cycle was calculated as 19.8 and 20.0 d, respectively. Two of the sows did not exhibit cyclic changes in any of the parameters measured, and on no occasion did either stand for service. In the second experiment, it was shown that estrus can be reliably induced in feral sows by either 1 of 2 methods: first, sows were induced to abort by prostaglandin injection. They were then administered gonadotrophin 48 to 72 h post abortion, and came into estrus 4 to 5 days later. Second, estrus was suppressed by feeding sows altrenogest, and was induced again about 9 days following altrenogest withdrawal.