Localization of the PGD and TGF beta-1 loci to pig chromosome 6q

Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012

Within two years of the re-discovery of Mendelism, Bateson and Saunders had described six traits in non-laboratory animals (five in chickens and one in cattle) that show single-locus (Mendelian) inheritance. In the ensuing decades, much progress was made in documenting an ever-increasing number of such traits. In 1987 came the first discovery of a causal mutation for a Mendelian trait in non-laboratory animals: a non-sense mutation in the thyroglobulin gene (TG), causing familial goitre in cattle. In the years that followed, the rate of discovery of causal mutations increased, aided mightily by the creation of genome-wide microsatellite maps in the 1990s and even more mightily by genome assemblies and single-nucleotide polymorphism (SNP) chips in the 2000s. With sequencing costs decreasing rapidly, by 2012 causal mutations were being discovered in non-laboratory animals at a rate of more than one per week. By the end of 2012, the total number of Mendelian traits in non-laboratory animals with known causal mutations had reached 499, which was half the number of published single-locus (Mendelian) traits in those species. The distribution of types of mutations documented in non-laboratory animals is fairly similar to that in humans, with almost half being missense or non-sense mutations. The ratio of missense to non-sense mutations in non-laboratory animals to the end of 2012 was 193:78. The fraction of non-sense mutations (78/271 = 0.29) was not very different from the fraction of non-stop codons that are just one base substitution away from a stop codon (21/61 = 0.34).

Association and expression study of MMP3, TGFβ1 and COL10A1 as candidate genes for leg weakness-related traits in pigs

The present study was aimed to determine the association between metalloproteinase 3 (MMP3), transforming growth factor beta 1 (TGFβ1) and collagen type X alpha I (COL10A1) gene polymorphisms with traits related to leg weakness in pigs. Three hundred Duroc × Pietrain cross breds (DuPi) and 299 pigs of a commercial population (CP) were used for the experiment. DuPi animals were examined for 10 different traits describing leg and feet structure, osteochondrosis (OC) scores and bone density status. Data of OC score at condylus medialis humeri, condylus medialis femoris and distal epiphysis ulna regions of CP were used for association analysis. Significant association (P < 0.05) was found for MMP3 SNP (g.158 C>T) with OC at head of femur and bone mineral density in the DuPi population. Association (P < 0.05) was found between SNP of TGFβ1 (g.180 G>A) with rear leg score and the principle component denoting both OC and feet and leg scores in the DuPi population. No association was found between COL10A1 (g.72 C>T) and leg weakness related traits. The associations of SNPs with OC traits could not be confirmed in the commercial population. Expression analysis of the three candidate genes was performed to compare between healthy and OC. TGFβ1 was found to be highly expressed (P < 0.05) in the OC compared to healthy cartilages, but no significant different expressions were observed for MMP3 and COL10A1 genes. The present finding suggested that TGFβ1 and MMP3 genes variants have an effect on some of the leg weakness related traits.

Quantitative trait loci analysis for leg weakness-related traits in a Duroc × Pietrain crossbred population

Background

Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs.

Methods

Three hundred and ten F₂ pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software.

Results

Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level.

Conclusions

Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs.

The porcine PGD gene is preferentially lost from chromosome 6 in pig x rodent somatic cell hybrids

The 6-phosphogluconate dehydrogenase (PGD) and glucose phosphate isomerase (GPI) genes are both located on chromosome 6 in the pig (Sus scrofa domestica). Nonetheless, the PGD gene was absent in a total of 17 GPI-positive cell lines found in three independently derived panels of pig x rodent somatic cell hybrids. In most of these cell lines we found an apparently normal pig chromosome 6 at cytogenetic analysis. These results suggest instability of the porcine PGD gene region in interspecies hybrid cells.

Chromosomal localization of the hormone sensitive lipase (LIPE) and insulin receptor (INSR) genes in pigs

Using rat hormone sensitive lipase (LIPE) and human insulin receptor (INSR) cDNA probes, the LIPE gene was assigned to chromosome 6p11-q21 and the INSR gene to chromosome 2q11-q21 in pigs by in situ hybridization. In humans, these two genes are located on the q and p arms of chromosome 19, respectively. The present results provide the first in situ hybridization mapping data for porcine chromosome 2.

cDNA cloning, mapping and polymorphism of the porcine Rhesus (RH) gene

The Rhesus (Rh) gene superfamily in humans and mice contains four independent genes, RH, RHAG, RHBG, and RHCG/GK. Heretofore, only the RHBG cDNA has been cloned in pig. We have isolated the porcine RH cDNA; its complete open reading frame of 1269 nucleotides encoded 423 amino acids. Porcine RH protein shared 67.6% amino acid identity with bovine RH, 61.0% with human RhCE and 60.8% with human RhD. The RT-PCR revealed RH transcripts in the spleen and bone marrow, but not in the heart, kidney, or lung. In RH intron 4, a deletion of 17 nucleotides distinguished the shorter allele (allele 1) from the longer. As determined in 115 unrelated pigs from five breeds - Landrace (L, n = 23), Large White (LW, n = 28), Duroc (D, n = 24), Hampshire (H, n = 20) and Piétrain (n = 20) - allele 1 frequencies were 1.0 (L, H), 0.77 (LW), 0.70 (P) and 0.25 (D). Somatic cell hybrid mapping localized the porcine RH and RHBG genes to pig chromosomes 6q22-q23 and 4q21-q22, respectively. Genetic mapping suggested RH-(FUT1, S, GPI, EAH, A1BG)-PGD as the most probable locus order. Sequence homology, mapping data, and haematopoietic tissue expression suggest that this cDNA may indeed encode the porcine RH homologue.

First international workshop on porcine chromosome 6. Report and abstracts

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

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 (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 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.

Porcine cytokines

Cytokines play a central role in modulation of immunological and physiological processes in animals under both homeostatic and abnormal conditions. Currently available information from a variety of species indicates that interleukins, interferons and tumor necrosis factor mobilize immune responses, activate inflammatory reactions and communicate with organ systems; colony stimulating factors regulate hematopoiesis and hematopoietic cell function; transforming growth factor beta affects wound healing, bone remodeling and cellular differentiation. Our understanding of cytokine biology in pigs is selective and based largely on effects of human proteins in porcine models of human diseases. However, knowledge of the nature and role of cytokines in swine immunology and physiology is increasing rapidly due to the application of molecular cloning techniques to porcine cytokines. This review summarizes the current state of knowledge of porcine cytokines and focuses on biological processes in which the porcine proteins have been investigated in swine.

Localization of the IGHG, PRKACB, and TNP2 genes in pigs by in situ hybridization

The porcine genes encoding the immunoglobulin gamma heavy chain (IGHG), cAMP-dependent protein kinase catalytic beta subunit (PRKACB), and transition protein 2 (TNP2) were mapped to Chromosomes (Chrs) 7 q25-q26, 6q31-q33, and 3p13-cent, respectively, by in situ hybridization. Localization of the IGHG gene confirms the assignment of linkage group III to Chr 7. Our results show that the IGHG locus in pigs, similar to the situation in other mammalian species, viz. humans, mouse, cattle, and river buffaloes, is located on the terminal region of the chromosome. The assignment of the PRKACB gene extends the homology observed between porcine Chr 6q and human Chr 1p. Mapping of the TNP2 gene provides the first marker assigned to the p arm of Chr 3 in pigs. The present study contributes to the development of the physical gene map in pigs and also bears significance in terms of comparative gene mapping.

Cosegregation of porcine malignant hyperthermia and a probable causal mutation in the skeletal muscle ryanodine receptor gene in backcross families

A study of the inheritance of malignant hyperthermia (MH) in the British Landrace breed revealed the same substitution of T for C at nucleotide 1843 in the ryanodine receptor (RYR1) gene that was previously shown to be correlated with MG in five Canadian swine breeds. Cosegregation of the mutation with MH in 338 informative meioses led to a lod score of 101.75 for linkage at Omax = 0.0. The substitution was also associated with a HinPI- BanII+ RsaI- haplotype in this breed, as in the five breeds tested earlier, suggesting its origin in a common founder animal. DNA-based detection of the MH status in 376 MH-susceptible heterozygous (N/n) and homozygous (n/n) pigs was shown to be accurate, eliminating the 5% diagnostic error that is associated with the halothane challenge test and flanking marker haplotyping procedures in current diagnostic use. These results strongly support the view that the substitution of T for C at nucleotide 1843 is the causative mutation in porcine MH and demonstrate the feasibility of rapid, accurate, noninvasive, large-scale testing for porcine MH status using DNA-based tests for the mutation.