Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia

Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

Transcriptional Profiling of Leucocyte Count Variation from Porcine Peripheral Blood Reveals Differential Gene Expression

Leucocytes have tremendous health-check importance related to the individual antiviral capacity of pigs and other mammals. However, the molecular mechanism of the immune response of blood leucocytes in pigs is not completely known. This study investigated the leucocyte-count variation before and after poly I:C stimulation in a Duroc–Erhualian F2 population. Pigs with increased and decreased differences in leucocyte counts were coded as increased responder (IR) and decreased responder (DR), respectively. Then, we used microarray technology to compare the gene-expression profiles of both groups of pigs. Transcriptomic analysis identified 129 differentially expressed genes (DEGs) in IR pigs and 136 DEGs in DR pigs. Forty-one common DEGs showed that both groups had similar expression patterns of immune responses. These results illustrated a differential expression in both groups. Furthermore, qPCR experiment was performed to verify the differential-expression profile. Functional annotation of the DEGs indicated that both IR and DR pigs were similar in several biological processes, including innate immune response, and also exhibited distinct differences in biological processes, molecular function, and pathways. These results provided insights into the mechanism underlying the antiviral capacity of pigs. Trial registration number is CAS Registry Number 24939-03-5.

Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs

Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. As more genomic data is being generated within different commercial or resource pig populations, the challenge which arises is how to collectively investigate the data with the purpose to increase sample size and implicitly the statistical power. This study performs an individual population GWAS, a joint population GWAS and a meta-analysis in three pig F2 populations. D1 is derived from European type breeds (Piétrain, Large White and Landrace), D2 is obtained from an Asian breed (Meishan) and Piétrain, and D3 stems from a European Wild Boar and Piétrain, which is the common founder breed. The traits investigated are average daily gain, backfat thickness, meat to fat ratio and carcass length. The joint and the meta-analysis did not identify additional genomic clusters besides the ones discovered via the individual population GWAS. However, the benefit was an increased mapping resolution which pinpointed to narrower clusters harboring causative variants. The joint analysis identified a higher number of clusters as compared to the meta-analysis; nevertheless, the significance levels and the number of significant variants in the meta-analysis were generally higher. Both types of analysis had similar outputs suggesting that the two strategies can complement each other and that the meta-analysis approach can be a valuable tool whenever access to raw datasets is limited. Overall, a total of 20 genomic clusters that predominantly overlapped at various extents, were identified on chromosomes 2, 7 and 17, many confirming previously identified quantitative trait loci. Several new candidate genes are being proposed and, among them, a strong candidate gene to be taken into account for subsequent analysis is BMP2 (bone morphogenetic protein 2).

Apulo-Calabrese and Crossbreed Pigs Show Different Physiological Response and Meat Quality Traits after Short Distance Transport

Simple Summary

Transport is a stressful procedure that can affect adversely the welfare of pigs and pork quality. It is well known that response to the journey is influenced by the genetic type. However, very little is known on the response of local breeds to the transport procedures despite the increasing interest in the welfare of animals during transport. The objective of this study was to investigate the effect of short distance transport on behaviour, blood parameters and meat quality traits of Apulo-Calabrese (local Italian pig breed) and crossbreed [Duroc × (Landrace × Large White)] pigs. Statistical analyses were done using univariate and multivariate approaches. Both approaches showed that glucose, albumin/globulin, urea, and aspartate aminotransferase concentrations were influenced by the genetic type. Despite at loading Apulo-Calabrese pigs were less reluctant to move and showed a lower vocalization, physiological response to the short distance transport was more intense in this breed when compared with crossbreeds. With regards to meat quality, higher a* and lower L* coordinates were found in Apulo-Calabrese which indicates darker and more reddish meat than crossbreeds. The results from this study may provide insight into the response of local breeds to the transport procedures.

Abstract

Despite the increasing interest in the welfare of animals during transport, very little is known on the response of local pig breeds to the transport procedures. This study aims to compare the effect of short journey on behaviour, blood parameters, and meat quality traits in 51 Apulo-Calabrese and 52 crossbreed [Duroc × (Landrace × Large White)] pigs. All the animals were blood sampled five days before delivery (basal condition) and at exsanguination for the analysis of creatine kinase, cortisol, glucose, lactate, albumin, albumin/globulin, total protein, urea, creatinine, aspartate aminotransferase (AST), alanine aminotransferase, alkaline phosphate, sodium, and potassium. Post mortem pH, color, drip loss, cooking loss, and Warner-Bratzler shear force were measured at different times in longissimus thoracis samples. Univariate and multivariate analyses showed that glucose, albumin/globulin, urea, and AST at exsanguination were influenced by the genetic type. Apulo-Calabrese showed the highest increase in blood values of lactate, creatinine, sodium and potassium after the short distance transport. Behavioural occurrences were similar in both genetic types during unloading and lairage. Small differences were observed for meat quality although significantly higher a* and lower L* were found in Apulo-Calabrese pigs, showing meat with a deeper red colour than crossbreeds.

Association between the splice mutation g.8283C>A of the PHKG1 gene and meat quality traits in Large White pigs

Pork technological and sensory qualities are greatly affected by water-holding capacity (WHC), pH, color, tenderness, and chemical composition, and the identification of genetic markers affecting these traits is regarded as a primary goal in pig selection. Phosphorylase Kinase Catalytic Subunit Gamma 1 (PHKG1) gene has been reported in the literature to be a candidate gene for meat drip loss, ultimate pH, color and glycolytic potential. This study was mainly aimed at testing whether PHKG1 g.8283C>A SNP was associated with meat quality traits in heavy pigs. The associations between PHKG1 g.8283C>A SNP, WHC, meat color and pH measurements were evaluated in 250 Italian Large White pigs. The marker showed an additive effect on WHC (P = .008) and a dominant effect on a* color parameter (P = .004). Further studies are needed to elucidate the effects of this polymorphism on heavy pig meat quality traits before this mutation could be considered a marker of interest for heavy pig selection schemes.

Polymorphism distribution of RYR1, PRKAG3, HFABP, MYF-5 and MC4R genes in crossbred pigs

This study was designed to screen the crossbred pigs for SNPs in five candidate genes, associated with pork quality traits and to differentiate their genotypes by PCR-RFLP. The results indicated that genotypes of crossbred pigs were NN (90%) and Nn (10%) for RYR1; RR (83%) and QR (17%) for PRKAG3; HH (98%), Hh (1%) and hh (1%) for HFABP; DD (99%) and CD (1%) for MYF-5; and AG (57%), GG (26%) and AA (17%) for MC4R SNPs, respectively. Allelic frequencies for five SNPs {RYR1 (1843C>T), PRKAG3 (c.599G>A), HFABP (c.1322C>T), MYF-5 (c.1205A>C) and MC4R (c.1426A>G)} were 0.95 and 0.05 (N/n), 0.08 and 0.92 (Q/R), 0.99 and 0.01 (H/h), 0.00 and 1.00 (C/D) and 0.45 and 0.55 (A/G), respectively. The effect of RYR1 (1843C>T) SNP was significant on pH₄₅ (P < 0.05), pH₂₄ (P < 0.05) and protein % (P < 0.05). The PRKAG3 (c.599G>A) and MC4R (c.1426A>G) SNP had significant association with dressing percentages. The results revealed that RYR1, PRKAG3 and MC4R SNPs may be used in marker associated selection for pork quality traits in crossbred pigs.

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report such a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. The deletion produces a truncated BBS9 protein expected to cause a complete loss-of-function, and we find a reduction of approximately 20% on the total number of piglets born from carrier by carrier matings. Homozygous del/del animals die mid- to late-gestation, as observed from high increase in numbers of mummified piglets resulting from carrier-by-carrier crosses. The moderate 10.8% carrier frequency (5.4% allele frequency) in this pig population suggests an advantage on a favourable trait in heterozygotes. Indeed, heterozygous carriers exhibit increased growth rate, an important selection trait in pig breeding. Increased growth and appetite together with a lower birth weight for carriers of the BBS9 null allele in pigs is analogous to the phenotype described in human and mouse for (naturally occurring) BBS9 null-mutants. We show that fetal death, however, is induced by reduced expression of the downstream BMPER gene, an essential gene for normal foetal development. In conclusion, this study describes a lethal 212kb deletion with pleiotropic effects on two different genes, one resulting in fetal death in homozygous state (BMPER), and the other increasing growth (BBS9) in heterozygous state. We provide strong evidence for balancing selection resulting in an unexpected high frequency of a lethal allele in the population. This study shows that the large amounts of genomic and phenotypic data routinely generated in modern commercial breeding programs deliver a powerful tool to monitor and control lethal alleles much more efficiently.

We report a large deletion within the BBS9 gene that induces late fetal mortality in homozygous affected animals in a commercial pig population. This late fetal mortality causes the fetus to become encapsulated and desiccated during the remaining time of the pregnancy, a process called mummification. The unusually high carrier frequency for this lethal deletion (10.8%) likely results from its strong positive association with growth rate in heterozygous individuals, an important selection trait in the pig breeding industry. Interestingly, we show that the positive effect on growth is induced by a heterozygous loss-of-function of the BBS9 gene, associated with obesity in human and mouse. However, late fetal mortality is induced by insufficient expression of the BMPER gene located directly downstream of the deletion which affects its regulatory elements required for gene expression. Together, our study shows an unique example of allelic pleiotropy in which one allele (deletion) is responsible for both increased growth and late fetal mortality by affecting two different genes.

A whole-genome sequence based association study on pork eating quality traits and cooking loss in a specially designed heterogeneous F6 pig population

To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits.

Malignant Hyperthermia: A Case Report in a Trauma Patient

Malignant hyperthermia is a rare condition that occurs in susceptible patients exposed to triggering anesthetic agents. It is associated with a high mortality rate if not recognized immediately and treated appropriately. A 52-year-old man presented to our clinic 2 days after an assault for management of jaw pain. A minimally displaced right parasymphyseal fracture and moderately displaced left body fracture of the mandible were diagnosed. There were no known drug allergies. The patient reported no previous difficulty with anesthesia, as well as no known prior adverse reactions to anesthesia in any relatives. The planned surgical intervention was open reduction-internal fixation of bilateral mandibular fractures. The patient received succinylcholine and desflurane during the procedure. A full 70 minutes elapsed before initial signs of hypermetabolism were noted, namely a rise in end-tidal carbon dioxide level. The patient received dantrolene sodium approximately 120 minutes after induction of anesthesia. Signs of hypermetabolism began to abate within 45 minutes of commencement of the malignant hyperthermia treatment protocol. He was subsequently transferred to the surgical intensive care unit for continued management and had a favorable postoperative course. This case underscores the importance of awareness of malignant hyperthermia and its presentation. This condition carries a potential high risk of complications after exposure to triggering anesthetic agents. Taking a complete and detailed history may help to identify potential cases. In this case, it was subsequently discovered that the patient's biological sister had a nearly fatal reaction to general anesthesia several years before this incident. Intraoperative vigilance in the monitoring of vital signs cannot be overemphasized. An increase in end-tidal carbon dioxide values, in addition to other clinical signs that cannot be easily attributed to other causes, should increase the clinical index of suspicion for a diagnosis of malignant hyperthermia.

Ryanodine receptor dysfunction in human disorders

Regulation of intracellular calcium (Ca²⁺) is critical in all cell types. The ryanodine receptor (RyR), an intracellular Ca²⁺ release channel located on the sarco/endoplasmic reticulum (SR/ER), releases Ca²⁺ from intracellular stores to activate critical functions including muscle contraction and neurotransmitter release. Dysfunctional RyR-mediated Ca²⁺ handling has been implicated in the pathogenesis of inherited and non-inherited conditions including heart failure, cardiac arrhythmias, skeletal myopathies, diabetes, and neurodegenerative diseases. Here we have reviewed the evidence linking human disorders to RyR dysfunction and describe novel approaches to RyR-targeted therapeutics.

Identification of an (AC)n microsatellite in the Six1 gene promoter and its effect on production traits in Pietrain × Duroc × Landrace × Yorkshire pigs

The Sine oculis homeobox 1 (Six1) gene is important for skeletal muscle growth and fiber specification; therefore, it is considered as a promising candidate gene that may influence porcine growth and meat quality traits. Nevertheless, the association of Six1 with these processes and the mechanisms regulating its expression remain unclear. The objectives of this study were to identify variant sites of Six1 in different pig breeds, conduct association analysis to evaluate the relationship between polymorphisms of these variants and porcine production traits in Pietrain × Duroc × Landrace × Yorkshire commercial pigs, and explore the potential regulatory mechanisms of Six1 affecting production traits. A total of 12 variants were identified, including 10 single- nucleotide variations (SNVs), 1 insertion- deletion (Indel), and 1 (AC)n microsatellite. Association analysis demonstrated that the SNV, g.1595A>G, was significantly associated with meat color (redness, a*); individuals with the G allele had greater a* values (P < 0.05). Moreover, our results demonstrated that the (AC)n polymorphism in the Six1 promoter was significantly associated with weaning weight (P < 0.05), carcass weight (P < 0.05), and thoracic and lumbar back fat (P < 0.01).In addition, we found that the (AC)n variant was closely related with Six1 expression levels and demonstrated this polymorphism on promoter activity by in vitro experiments. Overall, this study provides novel evidence for elucidating the effects of Six1 on porcine production traits as promising candidate and describes two variants with these traits, which are potential reference markers for pig molecular breeding. In addition, our data on the relationship between porcine Six1 expression and the polymorphic (AC)n microsatellite in its promoter may facilitate similar studies in other species.

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

Whole-genome resequencing reveals candidate mutations for pig prolificacy

Changes in pig fertility have occurred as a result of domestication, but are not understood at the level of genetic variation. To identify variations potentially responsible for prolificacy, we sequenced the genomes of the highly prolific Taihu pig breed and four control breeds. Genes involved in embryogenesis and morphogenesis were targeted in the Taihu pig, consistent with the morphological differences observed between the Taihu pig and others during pregnancy. Additionally, excessive functional non-coding mutations have been specifically fixed or nearly fixed in the Taihu pig. We focused attention on an oestrogen response element (ERE) within the first intron of the bone morphogenetic protein receptor type-1B gene (BMPR1B) that overlaps with a known quantitative trait locus (QTL) for pig fecundity. Using 242 pigs from 30 different breeds, we confirmed that the genotype of the ERE was nearly fixed in the Taihu pig. ERE function was assessed by luciferase assays, examination of histological sections, chromatin immunoprecipitation, quantitative polymerase chain reactions, and western blots. The results suggest that the ERE may control pig prolificacy via the cis-regulation of BMPR1B expression. This study provides new insight into changes in reproductive performance and highlights the role of non-coding mutations in generating phenotypic diversity between breeds.

Quantitative Proteomics and Phosphoproteomics Analysis Revealed Different Regulatory Mechanisms of Halothane and Rendement Napole Genes in Porcine Muscle Metabolism

Pigs with the Halothane (HAL) or Rendement Napole (RN) gene mutations demonstrate abnormal muscle energy metabolism patterns and produce meat with poor quality, classified as pale, soft, and exudative (PSE) meat, but it is not well understood how HAL and RN mutations regulate glucose and energy metabolism in porcine muscle. To investigate the potential signaling pathways and phosphorylation events related to these mutations, muscle samples were collected from four genotypes of pigs, wild type, RN, HAL, and RN-HAL double mutations, and subjected to quantitative proteomic and phosphoproteomic analysis using the TiO₂ enrichment strategy. The study led to the identification of 932 proteins from the nonmodified peptide fractions and 1885 phosphoproteins with 9619 phosphorylation sites from the enriched fractions. Among them, 128 proteins at total protein level and 323 phosphosites from 91 phosphoproteins were significantly regulated in mutant genotypes. The quantitative analysis revealed that the RN mutation mainly affected the protein expression abundance in muscle. Specifically, high expression was observed for proteins related to mitochondrial respiratory chain and energy metabolism, thereby enhancing the muscle oxidative capacity. The high content of UDP-glucose pyrophosphorylase 2 (UGP2) in RN mutant animals may contribute to high glycogen storage. However, the HAL mutation mainly contributes to the up-regulation of phosphorylation in proteins related to calcium signaling, muscle contraction, glycogen, glucose, and energy metabolism, and cellular stress. The increased phosphorylation of Ca²⁺/calmodulin-dependent protein kinase II (CAMK2) in HAL mutation may act as a key regulator in these processes of muscle. Our findings indicate the different regulatory mechanisms of RN and HAL mutations in relation to porcine muscle energy metabolism and meat quality.

Assessment of turkey vehicle container microclimate on transit during summer season conditions

This study evaluated the formed microclimate commercial truck transport practices effects on the turkeys' welfare by measuring Dead on Arrival (DOA) index and pale, soft, and exudative (PSE-like) meat occurrence. The experimental design was entirely randomized in a 6 × 2 factorial arrangements (two truck container compartments × six water shower groups) with birds positioned at superior front (SF), inferior front (IF), superior middle (SM), inferior middle (IM), superior rear (SR), and inferior rear (IR) and two bath treatments: with water shower (WiS) and without water shower (WoS) with eight replications for each treatment. The animals were transported for 95 min' journey from the farm to the slaughterhouse under hot-humidity conditions. The results shown herein indicated the formation of a thermal core at the inferior middle and rear truck container regions, because the heat produced by the birds and the influence of developed microclimate consisting of temperature, relative humidity, and air ventilation. The IM and IR container compartments under the WoS treatment presented the highest (P < 0.01) numbers of PSE-like meat incidence and DOA index values compared with those located at the front under WiS treatment as the consequence of the altered to birds unbearable conditions within the container microclimate in transit. The formed microclimate during the commercial transport practices under hot-humidity conditions affected the bird's welfare consequently turkey meat qualities.

In-transit development of color abnormalities in turkey breast meat during winter season

Background

The poultry industry suffers losses from problems as pale, soft and exudative (PSE), and dark, firm and dry (DFD) meat can develop in meat as a result of short- and long-term stress, respectively. These abnormalities are impacted by pre-slaughter animal welfare.

Methods

This work evaluated the effects of open vehicle container microclimate, throughout the 38 ± 10 km journey from the farm to the slaughterhouse, on commercially turkey transported during the Brazilian winter season. The journey was initiated immediately after water bath in truck fitted with portable Kestrel anemometers to measure air ventilation, relative humidity, temperature and ventilation.

Results

The inferior compartments of the middle and rear truck regions showed highest temperature and relative humidity, and lower air ventilation. In addition, the superior compartments of the front truck regions presented lower temperature and wind chill, and highest air ventilation. The breast meat samples from animals located at the inferior compartments of the middle and rear truck regions and subjected to with water bath (WiB) treatment presented highest DFD-like and had lowest PSE-like meat incidence than those from animals located at other compartments within the container. Lower incidence of PSE-like meat was observed in birds without water bath (WoB).

Conclusions

Assessment on turkeys transported under Brazilian southern winter conditions revealed that breast meat quality can be affected by relative humidity, air ventilation, temperature, and transport under subtropical conditions promoting color abnormalities and the formation of simultaneously PSE-like and DFD-like meat.

One century of genetic changes in pigs and the future needs

Breeding programmes and improved knowledge of genetics have resulted in gradually increased genetic changes in pigs. In this paper the genetic changes in the European pig during the last century are analysed and compared with societal needs for the following decades. Dutch data are used to support the general trend in Europe and results of an EC project on breeding and society are used to identify societal needs.

Genetic changes in pigs started early this century, mainly in Northern Europe, by the gradual set up of local and regional breeding programmes. In the first 60 years the goal of these programmes was focussed only on leanness and feed efficiency. However, type, leg quality and breed characteristics were of utmost importance in these years for some breeding programmes. During these decades the genetic changes were negligible for reproduction traits. Progress was achieved especially for breed characteristics like type and colour and later also backfat thickness, daily gain and consequently improved feed efficiency.

With the introduction of crosses in the early 60's, specialisation in dam and sire lines but moreover in breeding programmes arose in the pig industry. This specialisation resulted rapidly in increased genetic changes, more breeds and/or lines and breeding goals that supported efficient lean meat production systems. Especially in the sire lines, this specialisation resulted in increased progress for daily gain, backfat thickness and feed efficiency. Improved knowledge of genetics increased genetic changes in leanness and feed efficiency during the last few decades, but at the same time attention could be and was paid to fertility and vitality. During the last decade most European pig breeding programmes realised anual genetic progress for daily gain of +20 g/day, lean meat % of +0.5% and litter size of +0.2 piglet/litter. Molecular genetics does not enable more genetic change for these traits, but does so especially for expensive or difficult to measure traits, e.g. meat quality, health and longevity. In commercial pig breeding programmes selection limits have not been reached yet. Nevertheless, there are experimental results that indicate unintended side effects of the present breeding goals.

Next to changes in breeding possibilities, the societal needs have also changed. During the first 80–90 years of the century, pig producers were aiming at production of lean meat at low(er) prices. In this period low prices were more important than quality and/or welfare of the pigs. Nowadays, diversification in consumers' needs is growing and quality of the product (including production circumstances) is important in Western Europe. The market for pork is changing from a market of producers into a market of (potential) buyers. Clearly, the success of any pig breeding programme next century will be judged by the consumer. Where a newly bred, or genetically modified, variety of animal fails to provide something people are prepared to buy, the breeding programme will be judged a failure. In this respect ethical issues are also becoming more important. Modern breeding techniques can threaten animal welfare; a very fast increase in one or a few traits can easily result in an insufficient increase or adaptation of the organs and skeleton. Animal integrety is another important issue, especially related to genetically modified animals. Clearly, the relationship between animal and human interests is central to any view.

From the analysis of genetic changes in pigs and the present and foreseen changes in market demands, it may be concluded that the pig breeding programmes were very successful; but they will have to change their goals. Less emphasis will be needed on low cost price and more emphasis on product quality, biodiversity and well balanced genetic changes for economically important traits.

Candidate SNP of CACNA2D1 Gene Associated with Clinical Mastitis and Production Traits in Sahiwal (Bos taurus indicus) and Karan Fries (Bos taurus taurus × Bos taurus indicus)

The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association with clinical mastitis and production traits. Exon 18 and its flanking regions were screened for the presence of SNPs. Statistical analysis was performed to identify association of period of birth, breed, and genotype with mastitis incidence on randomly selected 103 Sahiwal and 102 Karan Fries cattle. PCR-RFLP analysis revealed that g.38819398G > A mutation in exon 18 (269 bp amplicon) of CACNA2D1 gene resolved into AA, AG, and GG genotypes in Sahiwal and Karan Fries cattle. Wald chi-square analysis revealed that the period of birth, breed, and genotype were significantly associated with mastitis incidence. GG genotyped cattle were found to be less susceptible to mastitis. Least square analysis revealed that GG and AG genotype animals of G38819398A SNP of CACNA2D1 gene in Sahiwal as well as in Karan Fries cattle were associated with higher average milk yields during 1st, 2nd, and 3rd lactations (P < 0.01). These observations and their differential association with the incidence of mastitis and production traits can be utilized as an aid to selection for simultaneous improvement of both antagonistic traits; however, validation of results on large number of animals is warranted.

Congenital myopathies: disorders of excitation-contraction coupling and muscle contraction

The congenital myopathies are a group of early-onset, non-dystrophic neuromuscular conditions with characteristic muscle biopsy findings, variable severity and a stable or slowly progressive course. Pronounced weakness in axial and proximal muscle groups is a common feature, and involvement of extraocular, cardiorespiratory and/or distal muscles can implicate specific genetic defects. Central core disease (CCD), multi-minicore disease (MmD), centronuclear myopathy (CNM) and nemaline myopathy were among the first congenital myopathies to be reported, and they still represent the main diagnostic categories. However, these entities seem to belong to a much wider phenotypic spectrum. To date, congenital myopathies have been attributed to mutations in over 20 genes, which encode proteins implicated in skeletal muscle Ca²⁺ homeostasis, excitation-contraction coupling, thin-thick filament assembly and interactions, and other mechanisms. RYR1 mutations are the most frequent genetic cause, and CCD and MmD are the most common subgroups. Next-generation sequencing has vastly improved mutation detection and has enabled the identification of novel genetic backgrounds. At present, management of congenital myopathies is largely supportive, although new therapeutic approaches are reaching the clinical trial stage.

UCP1-independent signaling involving SERCA2b-mediated calcium cycling regulates beige fat thermogenesis and systemic glucose homeostasis

Uncoupling protein 1 (UCP1) plays a central role in nonshivering thermogenesis in brown fat; however, its role in beige fat remains unclear. Here we report a robust UCP1-independent thermogenic mechanism in beige fat that involves enhanced ATP-dependent Ca2+ cycling by sarco/endoplasmic reticulum Ca2+-ATPase 2b (SERCA2b) and ryanodine receptor 2 (RyR2). Inhibition of SERCA2b impairs UCP1-independent beige fat thermogenesis in humans and mice as well as in pigs, a species that lacks a functional UCP1 protein. Conversely, enhanced Ca2+ cycling by activation of α1- and/or β3-adrenergic receptors or the SERCA2b-RyR2 pathway stimulates UCP1-independent thermogenesis in beige adipocytes. In the absence of UCP1, beige fat dynamically expends glucose through enhanced glycolysis, tricarboxylic acid metabolism and pyruvate dehydrogenase activity for ATP-dependent thermogenesis through the SERCA2b pathway; beige fat thereby functions as a 'glucose sink' and improves glucose tolerance independently of body weight loss. Our study uncovers a noncanonical thermogenic mechanism through which beige fat controls whole-body energy homeostasis via Ca2+ cycling.

The structural basis of ryanodine receptor ion channel function

Large-conductance Ca²⁺ release channels known as ryanodine receptors (RyRs) mediate the release of Ca²⁺ from an intracellular membrane compartment, the endo/sarcoplasmic reticulum. There are three mammalian RyR isoforms: RyR1 is present in skeletal muscle; RyR2 is in heart muscle; and RyR3 is expressed at low levels in many tissues including brain, smooth muscle, and slow-twitch skeletal muscle. RyRs form large protein complexes comprising four 560-kD RyR subunits, four ∼12-kD FK506-binding proteins, and various accessory proteins including calmodulin, protein kinases, and protein phosphatases. RyRs share ∼70% sequence identity, with the greatest sequence similarity in the C-terminal region that forms the transmembrane, ion-conducting domain comprising ∼500 amino acids. The remaining ∼4,500 amino acids form the large regulatory cytoplasmic "foot" structure. Experimental evidence for Ca²⁺, ATP, phosphorylation, and redox-sensitive sites in the cytoplasmic structure have been described. Exogenous effectors include the two Ca²⁺ releasing agents caffeine and ryanodine. Recent work describing the near atomic structures of mammalian skeletal and cardiac muscle RyRs provides a structural basis for the regulation of the RyRs by their multiple effectors.

Mitochondrial-nuclear crosstalk, haplotype and copy number variation distinct in muscle fiber type, mitochondrial respiratory and metabolic enzyme activities

Genes expressed in mitochondria work in concert with those expressed in the nucleus to mediate oxidative phosphorylation (OXPHOS), a process that is relevant for muscle metabolism and meat quality. Mitochondrial genome activity can be efficiently studied and compared in Duroc and Pietrain pigs, which harbor different mitochondrial haplotypes and distinct muscle fiber types, mitochondrial respiratory activities, and fat content. Pietrain pigs homozygous-positive for malignant hyperthermia susceptibility (PiPP) carried only haplotype 8 and showed the lowest absolute mtDNA copy number accompanied by a decrease transcript abundance of mitochondrial-encoded subunits ND1, ND6, and ATP6 and nuclear-encoded subunits NDUFA11 and NDUFB8. In contrast, we found that haplotype 4 of Duroc pigs had significantly higher mitochondrial DNA (mtDNA) copy numbers and an increase transcript abundance of mitochondrial-encoded subunits ND1, ND6, and ATP6. These results suggest that the variation in mitochondrial and nuclear genetic background among these animals has an effect on mitochondrial content and OXPHOS system subunit expression. We observed the co-expression pattern of mitochondrial and nuclear encoded OXPHOS subunits suggesting that the mitochondrial-nuclear crosstalk functionally involves in muscle metabolism. The findings provide valuable information for understanding muscle biology processes and energy metabolism, and may direct use for breeding strategies to improve meat quality and animal health.

Effects of single nucleotide polymorphisms and haplotypes of the protein kinase AMP-activated non-catalytic subunit gamma 3 (PRKAG3) gene on production, meat quality and carcass traits in Italian Large White pigs

PRKAG3 is a major gene for meat quality and production in pigs. In this study, we investigated two single nucleotide polymorphisms (SNPs) of the PRKAG3 promoter region (g.-995A>G and g.-311A>G) in 381 pigs of different breeds. Association between these SNPs and three major haplotypes, constructed including other three substitutions (c.89C>A, c.154A>G and c.595G>A) and different traits (meat quality parameters: pH_2h, pH_u, glycogen and lactate content, glycolytic potential and cathepsin B activity of Semimembranosus muscle; estimated breeding values and random residuals for growth performances and carcass traits) were analysed in 271 Italian Large White performance tested pigs. A significant effect (P=0.043) of the g.-995A>G SNP on cathepsin B activity and a suggestive effect (P=0.067) of the g.-311A>G SNP on pH_u were found. The haplotype [g.-995G:g.-311G:c.89A:c.154G:c.595G] was associated with pH_u (P=0.024), glycolytic potential (P=0.040) and cathepsin B activity (P=0.086). This study on haplotypes, including promoter region SNPs, contribute to explain the effect of this gene on meat quality traits in pigs.

Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle

DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS). Overall, 23150 differentially methylated regions (DMRs) were identified which were located in 8596 genes enriched in 9922 GO terms, of which 1046 GO terms were significantly enriched (p<0.05) including lipid translocation (GO: 0034204) and lipid transport (GO: 0015914). KEGG analysis showed that the DMR related genes were distributed among 276 pathways. Correlation analysis found that 331 DMRs were negatively correlated with the expression levels of differentially expressed genes (DEGs) with 21 DMRs located in promoter regions. Our results identified novel candidate DMRs and DEGs correlated with meat quality traits, which will be valuable for future genomic and epigenomic studies of muscle development and for marker assisted selection of meat quality traits.

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes.

Refining genomewide association for growth and fat deposition traits in an F pig population

The identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin () and myosin light chain, phosphorylatable, fast skeletal muscle () genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene () may be a candidate for the fat deposition trait signals on SSC6.

Genetic Factors Affecting Pork Quality: Halothane and Rendement Napole Genes

The most common pork quality problems are pale, soft, and exudative (PSE) and acid pork (AP). PSE is associated with the expression of recessive halothane (Hal) allele Halⁿ. Recessive Hal pigs (Halⁿⁿ) have defective Ca²⁺ release channels (CRC) or Ryanodine Receptors (RYR1) within the sarcoplasmic reticulum that allow uncontrolled release of Ca²⁺ in response to stress. Abnormal lactic acid metabolism caused by stress prior to slaughter leads to the sudden drop in postmortem muscle pH producing the PSE pork. Conversely, AP is caused by the dominant RN^- allele of the Rendement Napole gene. RN^- pigs have high glycolytic potential that causes the lower ultimate pH_u due to excessive lactic acid production postmortem. Poor water holding capacity of muscle cells in PSE and AP causes excessive drip loss leading to low cooking and processing yields. The conventional methods to evaluate Hal and RN genotypes are less effective compared to the more accurate gene marker tests. Selection against the Halⁿ and RN^- alleles by genomic selection can potentially reduce the frequencies of the defective genes with high accuracy in less time. As more quantitative trait loci (QTL) are identified, pig breeders are able to select traits more effectively to increase efficiency of pig production and enhance pork quality.

The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

Background

One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality.

Results

Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb–40.1 Mb) and two on chromosome 15 (58.5 Mb–60.5 Mb and 132 Mb–135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5.

Conclusions

Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes’ potential role on meat quality. The gained information can be used in later functional studies.

Association of a missense mutation in the positional candidate gene glutamate receptor-interacting protein 1 with backfat thickness traits in pigs

OBJECTIVE

Previously, we reported quantitative trait loci (QTLs) affecting backfat thickness (BFT) traits on pig chromosome 5 (SW1482-SW963) in an F2 intercross population between Landrace and Korean native pigs. The aim of this study was to evaluate glutamate receptor-interacting protein 1 (GRIP1) as a positional candidate gene underlying the QTL affecting BFT traits.

METHODS

Genotype and phenotype analyses were performed using the 1,105 F₂ progeny. A mixed-effect linear model was used to access association between these single nucleotide polymorphism (SNP) markers and the BFT traits in the F₂ intercross population.

RESULTS

Highly significant associations of two informative SNPs (c.2442 T>C, c.3316 C>G [R1106G]) in GRIP1 with BFT traits were detected. In addition, the two SNPs were used to construct haplotypes that were also highly associated with the BFT traits.

CONCLUSION

The SNPs and haplotypes of the GRIP1 gene determined in this study can contribute to understand the genetic structure of BFT traits in pigs.

Associations of biochemical changes and maternal traits with mutation 1843 (C>T) in the RYR1 gene as a common cause for porcine stress syndrome

Stress syndrome is usually caused by a mutation in the ryanodine receptor gene (ryr1) and it is widely studied in humans and swine populations. The protein product of this gene plays a crucial role in the regulation of calcium transport in muscle cells. A G>T mutation in the human ryr1 gene, which results in the replacement of a conserved arginine at position 614 where a leucine occurs at the same position as the previously identified Arg→Cys mutation reported in all cases of porcine stress syndrome (PSS). Porcine stress syndrome affects biochemical pathways in stress-susceptible individuals during a stress episode and some biochemical parameters that were used as markers for diagnostic purposes. Also, PSS has remarkable influence on the maternal characteristics of sows. This study dealt with different genotypes for PSS and its association with possible biochemical changes and maternal traits of sows. Seventy-three reproductive sows genotyped for PSS by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were included in this survey. Sixty of them were stress-free (NN), 11 were heterozygous carriers (Nn) and two animals were homozygous (nn) for the 1843 (C>T) mutation. Significant differences in non stress induced animals with different PSS genotypes were found in the values of creatine phoshokinase (CPK), lactate dehydrogenase (LDH), alkaline phosphatase (AP) and aspartate aminotransferase (AST). Regarding the maternal traits, our study showed that stress susceptible animals (nn) have an increased number of stillborn piglets and a reduced number of newborn piglets compared with heterozygous and normal animals.

Effects of Morphological Characteristics of Muscle Fibers on Porcine Growth Performance and Pork Quality

The aim of this study was to investigate the effects of morphological characteristics of porcine muscle fibers on growth performance, muscle fiber characteristics, and pork quality taken from the longissimus dorsi muscle. A total of 239 crossbred pigs (164 castrated males and 75 females) were used in this study. Experimental pigs were categorized by the total number of muscle fiber (TNF: High and Low) and cross sectional area of muscle fiber (CSAF: Large, Middle, and Small). Their combinations were classified into six groups (High-Large, HL; High-Middle, HM; High-Small, HS; Low-Large, LL; Low-Middle, LM; Low-Small, LS). The TNF and CSAF were significantly (p<0.05) correlated with growth rate and carcass productivity, while the only of the type I number had no meaningful relationships excluding the correlation with loin area (p<0.001). The proportion of type I area was positively correlated with pH_{45 min} while the proportion of type IIB area was negatively correlated with pH_{45 min} and pH_{24 h} (p<0.05). Drip loss and protein denaturation had strong relationships with the proportion of type IIB number or area. The HL group exhibited the greatest growth performance. In addition, the HL group had significantly greater values in protein solubility than the other groups. In conclusion, this study suggest that high TNF combined to large CSAF improve the ultimate lean meat productivity and assure normal meat quality simultaneously with increased both proportion of number and area of type I, type IIA muscle fibers and lowered proportion of number and area of type IIB.

Identification of candidate genes associated with porcine meat color traits by genome-wide transcriptome analysis

Meat color is considered to be the most important indicator of meat quality, however, the molecular mechanisms underlying traits related to meat color remain mostly unknown. In this study, to elucidate the molecular basis of meat color, we constructed six cDNA libraries from biceps femoris (Bf) and soleus (Sol), which exhibit obvious differences in meat color, and analyzed the whole-transcriptome differences between Bf (white muscle) and Sol (red muscle) using high-throughput sequencing technology. Using DEseq2 method, we identified 138 differentially expressed genes (DEGs) between Bf and Sol. Using DEGseq method, we identified 770, 810, and 476 DEGs in comparisons between Bf and Sol in three separate animals. Of these DEGs, 52 were overlapping DEGs. Using these data, we determined the enriched GO terms, metabolic pathways and candidate genes associated with meat color traits. Additionally, we mapped 114 non-redundant DEGs to the meat color QTLs via a comparative analysis with the porcine quantitative trait loci (QTL) database. Overall, our data serve as a valuable resource for identifying genes whose functions are critical for meat color traits and can accelerate studies of the molecular mechanisms of meat color formation.

Gain of function AMP-activated protein kinase γ3 mutation (AMPKγ3R200Q) in pig muscle increases glycogen storage regardless of AMPK activation

Chronic activation of AMP‐activated protein kinase (AMPK) increases glycogen content in skeletal muscle. Previously, we demonstrated that a mutation in the ryanodine receptor (RyR1^R615C) blunts AMPK phosphorylation in longissimus muscle of pigs with a gain of function mutation in the AMPKγ3 subunit (AMPKγ3^R200Q); this may decrease the glycogen storage capacity of AMPKγ3^R200Q + RyR1^R615C muscle. Therefore, our aim in this study was to utilize our pig model to understand how AMPKγ3^R200Q and AMPK activation contribute to glycogen storage and metabolism in muscle. We selected and bred pigs in order to generate offspring with naturally occurring AMPKγ3^R200Q, RyR1^R615C, and AMPKγ3^R200Q + RyR1^R615C mutations, and also retained wild‐type littermates (control). We assessed glycogen content and parameters of glycogen metabolism in longissimus muscle. Regardless of RyR1^R615C, AMPKγ3^R200Q increased the glycogen content by approximately 70%. Activity of glycogen synthase (GS) without the allosteric activator glucose 6‐phosphate (G6P) was decreased in AMPKγ3^R200Q relative to all other genotypes, whereas both AMPKγ3^R200Q and AMPKγ3^R200Q + RyR1^R615C muscle exhibited increased GS activity with G6P. Increased activity of GS with G6P was not associated with increased abundance of GS or hexokinase 2. However, AMPKγ3^R200Q enhanced UDP‐glucose pyrophosphorylase 2 (UGP2) expression approximately threefold. Although UGP2 is not generally considered a rate‐limiting enzyme for glycogen synthesis, our model suggests that UGP2 plays an important role in increasing flux to glycogen synthase. Moreover, we have shown that the capacity for glycogen storage is more closely related to the AMPKγ3^R200Q mutation than activity.

RYR1-related rhabdomyolysis: A common but probably underdiagnosed manifestation of skeletal muscle ryanodine receptor dysfunction

Mutations in the skeletal muscle ryanodine receptor (RYR1) gene are associated with a wide spectrum of inherited myopathies presenting throughout life. Malignant hyperthermia susceptibility (MHS)-related RYR1 mutations have emerged as a common cause of exertional rhabdomyolysis, accounting for up to 30% of rhabdomyolysis episodes in otherwise healthy individuals. Common triggers are exercise and heat and, less frequently, viral infections, alcohol and drugs. Most subjects are normally strong and have no personal or family history of malignant hyperthermia. Heat intolerance and cold-induced muscle stiffness may be a feature. Recognition of this (probably not uncommon) rhabdomyolysis cause is vital for effective counselling, to identify potentially malignant hyperthermia-susceptible individuals and to adapt training regimes. Studies in various animal models provide insights regarding possible pathophysiological mechanisms and offer therapeutic perspectives.

Feeding patterns, growth performance and carcass traits in group-housed growing-finishing pigs: the effect of terminal sire line, halothane genotype and age

The effects of terminal sire line, halothane genotype and age on feeding patterns and growth performance were studied in 208 castrated growing-finishing pigs distributed in two batches. In batch 1 (no. = 130), pigs came from crosses of NN Landrace × Large White sows with a Pietrain Nn (Pi-Nn) or a Large White × Pietrain Nn terminal sire line (LwPi-Nn). In batch 2 (no. = 78), the same sows were used but crossed with three different terminal sire lines : a Pietrain nn (Pi-nn), and two Pietrain NN (Pi-NNa and Pi-NNb). Growth performance and feeding patterns of the progeny (Nn or NN for the halothane gene) were measured from 67 to 166 days of age. Pigs were housed in groups of 10 and 13 individuals in Batch 1 and 2, respectively, with a random mixed-breed and halothane genotype sample in each group (space allowance 1·3 m2 per pig and 1·1 m2 per pig, respectively). Feeding patterns were monitored with a computerized food intake recording system (IVOG®-station) and every 3 weeks pigs were weighed and backfat and loin-muscle depth were ultrasonically recorded (PIGLOG®). Carcass quality was assessed with the Fat-o-Meater grading probe. In batch 1, halothane genotype did not have a significant effect on any of the feeding patterns recorded, but Nn individuals had a significantly higher body weight (P <0·05), loin-muscle depth (P <0·05) and lower backfat thickness (P <0·01) in the last measurement taken, 3/4 carcass loin depth (P <0·05) and lower carcass last rib backfat (P <0·05) than NN pigs. Terminal sire line had a significant effect on all feeding patterns recorded except for feeding rate, Pi-Nn sired pigs showing a significantly higher food intake per visit (P <0·05) and feeder occupation time per visit (P <0·05) and lower number of visits (P <0·001) compared with LwPi-Nn sired pigs which, in turn, showed significantly higher food intake per day (P <0·001) and feeder occupation time per day (P <0·01). Terminal sire also affected growth performance and body composition, Pi-Nn sired pigs having a significantly lower body weight (P <0·001) and backfat thickness (P <0·001) but higher killing-out proportion and 3/4 loin depth (P <0·01) than LwPi-Nn sired pigs. In batch 2, Pi-NNb sired pigs showed a significantly lower food intake per day compared with the progeny of the other two terminal sires lines at some of the age measurements taken (P <0·05). The rest of the feeding patterns was not affected by terminal sire line. Body and carcass weights were also significantly lower (P <0·01) for Pi-NNb sired pigs, but their killing-out proportion was higher than Pi-NNa sired pigs. With regard to these variables, Pi-nn sired pigs held an intermediate position between the two NN terminal sire lines. In both batches, age was associated with a significant increase in food intake per visit and per day and feeding rate (P <0·001) and a decrease in feeder occupation time per visit and per day and frequency of visits to the feeder (P <0·001). Overall, the present results suggest differences between terminal sire lines for feeding patterns and confirm their evolution with age from short and frequent meals to long and larger ones in growing-finishing pigs. Under our conditions, the effects of terminal sire line on feeding patterns and growth performance surpassed those of the halothane genotype.

Prediction of carcass lean content by real-time ultrasound in Pietrain and negative stress Pietrain

Real-time ultrasound data of backfat thickness, longissimus muscle depth and longissimus area were carried out on 335 pigs (164 gilts and 171 barrows) using the Pie Medical Scanner 200 equipped with an ASP-18 probe and 3·5 MHz to predict carcass lean content in positive stress Pietrain (TT) and negative stress Pietrain (CC or CT). They were given food ad libitum and slaughtered at an average age of 213 days and an average weight of 101 kg. The day before slaughter, longitudinal and transverse images were taken at the last rib. After slaughter, the lean meat content was estimated by a CGM (capteur gras-maigre) equipped with an 8-mm diameter Sydel probe. The carcass lean proportion was higher in homozygote TT than homozygote CC and heterozygote CT individuals (P < 0·05). Gilts had more lean meat than barrows (P < 0·05). The correlation between the lean meat proportion and ultrasound backfat thickness (UBFT) or ultrasound longissimus muscle depth (ULMD) respectively was moderate. The prediction of lean meat proportion using UBFT, ULMD and ULMA gave an R2 which varied from 0·35 to 0·79. Real-time ultrasound is a tool that could potentially be used to predict the composition of pig carcasses before slaughter particularly if measurements can be taken with a higher degree of accuracy than at present.

Predicting population gene frequency from sample data

With an increase in the number of candidate genes for important traits in livestock, effective strategies for incorporating such genes into selection programmes are increasingly important. Those strategies in part depend on the frequency of a favoured allele in a population. Since comprehensive genotyping of a population is seldom possible, we investigate the consequences of sampling strategies on the reliability of the gene frequency estimate for a bi-allelic locus. Even within a subpopulation or line, often only a proportion of individuals will be genotype tested. However, through segregation analysis, probable genotypes can be assigned to individuals that themselves were not tested, using known genotypes on relatives and a starting (presumed) gene frequency. The value of these probable genotypes in estimation of gene frequency was considered. A subpopulation or line was stochastically simulated and sampled at random, over a cluster of years or by favouring a particular genotype. Line was simulated (replicated) 1000 times. The reliability of gene frequency estimates depended on the sampling strategy used. With random sampling, even when a small proportion of a line was genotyped (0·10), the gene frequency of the population was well estimated from the across-line mean. When information on probable genotypes on untested individuals was combined with known genotypes, the between-line variance in gene frequency was estimated well; including probable genotypes overcame problems of statistical sampling. When the sampling strategy favoured a particular genotype, unsurprisingly the estimate of gene frequency was biased towards the allele favoured. In using probable genotypes the bias was lessened but the estimate of gene frequency still reflected the sampling strategy rather than the true population frequency. When sampling was confined to a few clustered years, the estimation of gene frequency was biased for those generations preceding the sampling event, particularly when the presumed starting gene frequency differed from the true population gene frequency. The potential risks of basing inferences about a population from a potentially biased sample are discussed.