Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype

Expression and structural analysis of taste receptor genes in Iberian and Duroc pigs

BACKGROUND

Taste receptor genes are expressed in sensory cells located in the tongue and influence food preferences, voluntary feed intake, and other relevant traits. Taste perception may differ between livestock breeds that show differences in eating behaviour and between animals that receive different diets or show phenotypic variation in feed intake or related-traits. The objectives of this work were to deepen the understanding of the regulation of the function of taste receptor genes in the circumvallate papillae of obese Iberian pigs in comparison to Duroc pigs, and to characterize their genetic variation and associations with relevant production traits.

RESULTS

We performed a gene expression and structural analysis of ten taste receptor genes in Iberian and Duroc pigs. Gene expression was quantified in the circumvallate papillae of 48 growing Iberian and Duroc pigs maintained under identical management conditions but fed isocaloric diets differing in energy source: either high concentration of fat rich in oleic acid (HO) or carbohydrates (CH); and sacrificed after 47 days of treatment (50.5 kg live weight). Gene expression differed between the two breeds for most of the analyzed genes, with the TAS1R1, TAS1R2, TAS1R3, TAS2R4, TAS2R38, TAS2R39, GPR84, and CD36 genes being overexpressed in Duroc pigs. The diet effect was modulated by breed, with TAS1R1, TAS1R3, and TAS2R4 genes being overexpressed only in Duroc pigs fed the HO diet. Detection of genetic variants (single nucleotide polymorphisms, SNPs) for this panel of genes was performed on muscle RNA-seq data, and three SNPs in the TAS1R1, TAS1R3, and CD36 genes were selected for association studies. All three SNPs were associated with various growth, fattening, tissue fat content, and composition traits. Moreover, the CD36:c.910G/T SNP was associated with oral CD36 gene expression and with differences in the predicted mRNA secondary structure.

CONCLUSIONS

Most taste receptor genes are expressed at lower level in circumvallate papillae from Iberian than Duroc pigs. This aligns with lower overall taste sensitivity, higher feed intake, and obese nature of Iberian pigs. Significant association results were observed for SNPs in the TAS1R1 and TAS1R3 genes with meat quality traits and liver composition, which showed segregation in world-wide distributed breeds, but particularly for a potential causal SNP in the CD36 gene, associated with growth and tissue composition, which segregates in Iberian populations.

The impact of host genetics on porcine gut microbiota composition excluding maternal and postnatal environmental influences

The gut microbiota of the pig is being increasingly studied due to its implications for host homeostasis and the importance of the pig as a meat source and biomedical model of human diseases. However, most studies comparing the microbiome between different breeds do not consider the influence of maternal environment during the colonization of the microbiota. The aim of the present study was to compare the gut microbiota during postnatal growth between two pig genotypes (purebred Iberian vs. crossbreds Iberian x Large White pigs), gestated in a single maternal environment (pure Iberian mothers) inseminated with heterospermic semen. Postnatally, piglets were maintained in the same environmental conditions, and their microbiota was studied at 60 and 210 days old. Results showed that age had the greatest influence on alpha and beta diversity, and genotype also affected beta diversity at both ages. There were differences in the microbiome profile between genotypes at the ASV and genus levels when jointly analyzing the total number of samples, which may help to explain phenotypical differences. When each time-point was analyzed individually, there were more differences at 210 days-old than 60 days-old. Fecal short-chain fatty acids (SCFA) were also affected by age, but not by genotype. These results may be a basis for further research on host genotype interactions with the gut microbiota.

Maternal dietary antioxidant supplementation regulates weaned piglets' adipose tissue transcriptome and morphology

Antioxidant supplementation in critical periods may be useful for improvement of piglet early viability and development. We have evaluated the effects of maternal perinatal diet inclusion of a high vitamin E level (VE, 100 mg all-rac-α-tocopheryl acetate /kg), hydroxytyrosol (HT, 1.5 mg/kg), or their combination (VEHT), in comparison to a control diet (C, 30 mg all-rac-α-tocopheryl acetate /kg), on the offspring homeostasis and metabolism, analysing the weaned piglets' adipose tissue transcriptome and adipocyte morphology. Diets were provided to pregnant Iberian sows (n = 48, 12 per treatment) from gestation day 85 to weaning (28 days postpartum) and 48 piglets (n = 12 per treatment) were sampled 5 days postweaning for dorsal subcutaneous adipose tissue analyses. RNA obtained from 6 animals for each diet was used for paired-end RNA sequencing. Results show that supplementation of sows' diet with either vitamin E or hydroxytyrosol had substantial effects on weaned piglet adipose transcriptome, with 664 and 587 genes being differentially expressed, in comparison to C, respectively (q-value<0.10, Fold Change>1.5). Genes upregulated in C were mainly involved in inflammatory and immune response, as well as oxidative stress, and relevant canonical pathways and upstream regulators involved in these processes were predicted as activated, such as TNF, IFNB or NFKB. Vitamin E, when supplemented alone at high dose, activated lipid biosynthesis functions, pathways and regulators, this finding being accompanied by increased adipocyte size. Results suggest an improved metabolic and antioxidant status of adipose tissue in animals born from sows supplemented with individual antioxidants, while the combined supplementation barely affected gene expression, with VEHT showing a prooxidant/proinflamatory functional profile similar to C animals. Different hypothesis are proposed to explain this unexpected result. Findings allow a deeper understanding of the processes taking place in adipose tissue of genetically fat animals and the role of antioxidants in the regulation of fat cells function.

Impact of the leptin receptor gene on pig performance and quality traits

The recessive T allele of the missense polymorphism rs709596309 C > T of the leptin receptor gene is associated with intramuscular fat. However, its overall impact on pork production is still partial. In this work, we investigated the all-round effects of the TT genotype on lean growth efficiency and carcass, meat and fat quality using data from an experiment that compared the performance of 48 TT and 48 C- (24 CT and 24 CC) Duroc barrows. The TT pigs were less efficient for lean growth than the C- pigs. Although heavier, their carcasses had less lean content, were shorter and had lighter loins. Apart from increasing marbling and saturated fatty acid content, changes caused by the TT genotype in meat and fat quality are likely not enough to be perceived by consumers. The effect on visual marbling score exceeded that on intramuscular fat content, which suggests a direct influence of the T allele on the pattern of fat distribution in muscle. With current low-protein diets, the T allele is expected to be cost-effective only in niche markets where a very high level of marbling is critical.

Transcriptomic Profiling of Subcutaneous Backfat in Castrated and Intact Alentejano Pigs Finished Outdoors with Commercial and Fiber-Rich Diets

In this work, we studied the backfat transcriptome of surgically castrated (C), intact (I) and intact fed an experimental diet (IE) outdoor-reared male Alentejano (AL) pigs. The experimental diet was a high-fiber diet with locally produced legumes and by-products associated with a boar taint reduction effect. At slaughter (~160 kg), backfat samples were collected for total RNA sequencing. Intact pigs presented leaner carcasses, more total collagen, and more unsaturated intramuscular fat content than C animals. A total of 2726 differentially expressed genes (DEGs, |log2 FC|> 0.58, q < 0.05) were identified between C and I with overexpressed genes related to muscular activity (MYH1, ACTA1) or collagen metabolism (COL1A1, COL1A2) in I pigs. Between C and IE, 1639 DEGs of genes involved in lipidic metabolism (LEP, ME1, FABP4, ELOVL6) were overexpressed in C. Finally, only 28 DEGs were determined between I and IE. Clustering results indicated a drastic influence of the testis in the transcriptome of subcutaneous fat of AL pigs, while the diet had a marginal effect. Diet can reduce stress by increasing satiety in animals, and could have induced an increase of skatole degradation due to the higher expression of the CYP2A19 gene in the IE group.

Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing

Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.

SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs

Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as LEPR, ACACA, FTO, LIPE or SCD on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as LRIG3, DENND1B, SOWAHB, EPHX1 or NFE2L2 affecting body weight, average daily gain and adiposity at different ages, or KRT10, NLE1, KCNH2 or AHNAK affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits.

Hypothalamic transcriptome analysis reveals male-specific differences in molecular pathways related to oxidative phosphorylation between Iberian pig genotypes

The hypothalamus is implicated in controlling feeding and adiposity, besides many other physiological functions, and thus can be of great importance in explaining productive differences between lean and fatty pig breeds. The present study aimed to evaluate the hypothalamic transcriptome of pure Iberian (IBxIB) and Large White x Iberian crossbreds (IBxLW) at 60 days-old, produced in a single maternal environment. Results showed the implication of gender and genotype in the hypothalamic transcriptome, with 51 differentially expressed genes (DEGs) between genotypes and 10 DEGs between genders. Fourteen genotype by sex interactions were found, due to a higher genotype effect on transcriptome found in males. In fact, just 31 DEGs were identified when using only females but 158 using only males. A higher expression of genes related to mitochondrial activity in IBxIB male animals (ND3, ND4, ND5, UQCRC2 and ATP6) was found, which was related to a higher oxidative phosphorylation and greater reactive oxygen species and nitric oxide production. IBxLW male animals showed higher expression of SIRT3 regulator, also related to mitochondrial function. When females were analysed, such differences were not found, since only some differences in genes related to the tricarboxylic acid cycle. Thus, the results indicate a significant effect and interaction of the breed and the sex on the hypothalamic transcriptome at this early age.

The neuroendocrine pathways and mechanisms for the control of the reproduction in female pigs

Within the hypothalamic-pituitary-gonad (HPG) axis, the major hierarchical component is gonadotropin-releasing hormone (GnRH) neurons, which directly or indirectly receive regulatory inputs from a wide array of regulatory signals and pathways, involving numerous circulating hormones, neuropeptides, and neurotransmitters, and which operate as a final output for the brain control of reproduction. In recent years, there has been an increasing interest in neuropeptides that have the potential to stimulate or inhibit GnRH in the hypothalamus of pigs. Among them, Kisspeptin is a key component in the precise regulation of GnRH neuron secretion activity. Besides, other neuropeptides, including neurokinin B (NKB), neuromedin B (NMB), neuromedin S (NMS), α-melanocyte-stimulating hormone (α-MSH), Phoenixin (PNX), show potential for having a stimulating effect on GnRH neurons. On the contrary, RFamide-related peptide-3 (RFRP-3), endogenous opioid peptides (EOP), neuropeptide Y (NPY), and Galanin (GAL) may play an inhibitory role in the regulation of porcine reproductive nerves and may directly or indirectly regulate GnRH neurons. By combining data from suitable model species and pigs, we aim to provide a comprehensive summary of our current understanding of the neuropeptides acting on GnRH neurons, with a particular focus on their central regulatory pathways and underlying molecular basis.

Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds

Background

Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds.

Methods

Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10^–6 and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model.

Results

We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN.

Conclusions

Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00671-w.

Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Simple Summary

Screening and interpretation of differentially expressed genes and associated biological pathways was conducted among experimental groups with divergent phenotypes providing valuable information about the metabolic events occurring and identification of candidate genes with major regulation roles. This comparative transcriptomic analysis includes the first RNA-seq analysis of the Longissimus lumborum muscle tissue from two Portuguese autochthonous pig breeds with different genetic backgrounds, Alentejano and Bísaro. Moreover, a complementary candidate gene approach was employed to analyse, by real time qPCR, the expression profile of relevant genes involved in lipid metabolism, and therefore with potential impacts on meat composition. This study contributes to explaining the biological basis of phenotypical differences occurring between breeds, particularly the ones related to meat quality traits that affect consumer interest.

Abstract

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

Effects of L-Glutamine Supplementation during the Gestation of Gilts and Sows on the Offspring Development in a Traditional Swine Breed

Simple Summary

Nutritional strategies during pregnancy in swine production are considered essential to increase the number of piglets born alive and improve their survival and development. Amino acids, such as glutamine, are among the best compound to introduce in commercial farms after obtaining positive results in trials carried out in selected swine breeds. However, several critical productive factors have to be assessed before translating these strategies to the farm level to ensure the best balance between benefits and investments. The current study focused on the effects of prenatal L-glutamine supplementation on the offspring of Iberian gilts and sows under farm conditions. It is the first trial of amino acid supplementation during pregnancy carried out in traditional swine breeds. These non-selected swine breeds show productive or physiological differences that could affect the supplementation effect. Indeed, although there were changes at the molecular and tissue level, these effects did not turn into advantageous effects for the offspring of traditional breeds. The present study shows the importance of pre-testing nutritional strategies under the final conditions and breeds of implementation and the need to deepen at the molecular level to improve the biological interpretation of findings.

Abstract

The use of amino acids during pregnancy, such as glutamine (Gln), seems to be a promising strategy in selected swine breeds to improve the offspring prenatal development. The main goal of the current study was to assess the development of the offspring from parity 1–3 sows of a traditional breed, which were supplemented with 1% glutamine after Day 35 of gestation, under farm conditions. A total of 486 (288 treated) piglets from 78 (46 treated) Iberian sows were used. At birth and slaughterhouse, fatty acid composition, metabolism, and mTOR pathway gene expression were analyzed. At birth, treated newborns showed greater amounts of specific amino acids in plasma, such as glutamine, asparagine, or alanine, and Σn-3 fatty acids in cellular membranes than control newborns. The expression of genes belonging to mTOR Complex 1 was also higher in treated piglets with normal birth-weight. However, these findings did not improve productive traits at birth or following periods in litters from supplemented gilts (parity 1) or sows (parities 2–3). Thus, further research is needed to properly understand the effects of prenatal glutamine supplementation, particularly in traditional swine breeds.

The Role of Offspring Genotype-By-Sex Interactions, Independently of Environmental Cues, on the Phenotype Traits of an Obese Swine Model

Simple Summary

The present study, comparing the postnatal development of purebred Iberian and crossbreds Iberian × Large White littermates born from purebred Iberian sows, allows us to discern phenotype traits driven by the genotype from features imposed by pre- and postnatal environment. The results obtained in this study support the well-known relevance of genotype but also evidence a paramount role of the interaction sex-by-genotype, with differential effects depending on the offspring genotype and sex.

Abstract

The present study aimed to assess the importance of offspring genotype on postnatal development, independently of confounding factors related to prenatal environment and postnatal lifestyle, using a translational model of obesity and metabolic syndrome (the Iberian pig). Hence, we compared two genotypes (purebred Iberian and crossbreds Iberian × Large White), produced in one single maternal environment (pure Iberian mothers) through artificial insemination of Iberian sows with Iberian and Large White heterospermic semen and maintained in the same conditions during postnatal development. The results indicate that, under same pre- and postnatal environments, the interaction genotype-by-sex has a determinant role on offspring phenotype (i.e., growth and development, metabolic and antioxidant status and fatty acid composition of different tissues). These results may set the basis for future preclinical and clinical research on the differences in the metabolic phenotype among genotypes.

Unraveling molecular mechanisms involved in the development of leptin resistance using the pig as a model

The increase in obesity worldwide underlines the need for research concerning its metabolic and genetic determinants. One of the most intriguing mechanisms regarding obesity involves leptin and its signaling cascade. Leptin is a key regulator contributing to the fine-tuned crosstalk between nutrient availability and appetite signaling in the central nervous system. Owing to ethical concerns, many human tissues are not readily available and pigs can serve as a good animal model owing to their comparable anatomy, metabolism and genetics. In the present study, we utilized the pig to investigate the possible impact of increased adiposity on the development of alterations within the leptin signaling pathway. Two divergent groups of pigs (High and Low) were defined based on a high and low amount of mesenteric fat. Cortex, cerebellum, hypothalamus, mesenteric, subcutaneous and retroperitoneal fat tissues were used to study changes in expression levels of 94 mRNA transcripts related to the leptin signaling pathway using the qPCR approach. No significant differences were found at the central nervous system, whereas the expression level of STAT1 was reduced in mesenteric fat and leptin (LEP) and interleukin 6 (IL6) were shown to be consistently increased in all analyzed fat compartments from pigs with a high amount of mesenteric fat. These results could imply the onset of leptin and pro-inflammatory cytokine overexpression at early stages of obesity in the analyzed pigs without affecting any key components in the central nervous system. Thus, these pigs showing a unique leptin deregulation in adipose tissues could be a useful translational resource for studies of obesity and leptin resistance phenotypes.

Differential Effects of Litter Size and Within-Litter Birthweight on Postnatal Traits of Fatty Pigs

Simple Summary

The current work evaluated the relative effects of the number of piglets in the litter of origin (high vs. low litter size) and the birthweight (low (LBW) vs. normal (NBW) in large litters) on postnatal performance and quality of carcasses and meat in purebred Iberian pigs. The results indicated that NBW piglets born in large litters had disparities in developmental patterns in weight and size, back-fat deposition, and fatty acid composition of viscerae compared to NBW piglets from small litters, which again were different from those found in LBW piglets when compared to their NBW counterparts. However, both growth patterns were altered and might indicate previous phases of metabolic disorders.

Abstract

Fatty pigs are characterized by a thrifty genotype, adapted to harsh environments based on changes in metabolism and energy saving. Thus, we hypothesized that feto-maternal energy partitioning in large litters might have postnatal effects that might be independent of intrauterine growth restriction (IUGR) processes. Hence, the current work reported the influence of two effects on postnatal performance and carcass and meat quality of purebred Iberian pigs: (a) the effects of the number of piglets in the litter (high vs. low litter size), and (b) the effects of birthweight (low (LBW) vs. normal (NBW)) in large litters. The results confirmed that NBW piglets born in large litters had differences in developmental patterns of weight, back-fat deposition, and fatty acid (FA) composition when compared to NBW piglets from small litters. These results were different from those found in LBW piglets when compared to their NBW counterparts, which showed an initial asymmetrical growth and altered muscle FA composition at slaughtering. The assessment of FA composition indicated better metabolic status in NBW piglets from large litters than in LBW piglets. These data support the concept that the prenatal environment, even when the individual may cope with it, inescapably affects postnatal life.

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with ~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.

pCADD: SNV prioritisation in Sus scrofa

BACKGROUND

In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes.

RESULTS

To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation.

CONCLUSIONS

We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.

Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

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.

Effects of fetal genotype and sex on developmental response to maternal malnutrition

The present study aimed to determine whether developmental patterns, adiposity level and fatty-acid composition of fetuses exposed to maternal malnutrition are driven by their sex or their genotype, or both, as these may modulate the adaptive response to the intrauterine environment independently of the maternal genotype. We used a single maternal genotype (purebred Iberian (IB) sows), which was inseminated with heterospermic semen (obtained by mixing semen from Iberian and Large White (LW) boars), to obtain four different subsets of fetuses (male and female, purebred (IB×IB) and crossbred (IB×LW)) in Iberian purebred sows. Analysis of fetal phenotypes indicated a better adaptive response of the female offspring, which was modulated by their genotype. When faced with prenatal undernutrition, females prioritised the growth of vital organs (brain, liver, lungs, kidneys and intestine) at the expense of bone and muscle. Moreover, the analysis of fat composition showed a higher availability of essential fatty acids in the female sex than in their male counterparts and also in the Iberian genotype than in crossbred fetuses. These results are of high translational value for understanding ethnic differences in prenatal programming of postnatal health and disease status, and show evidence that prenatal development and metabolic traits are primarily determined by fetal sex and strongly modulated by fetal genotype.

Modulatory Effects of Breed, Feeding Status, and Diet on Adipogenic, Lipogenic, and Lipolytic Gene Expression in Growing Iberian and Duroc Pigs

Meat quality depends on tissue composition which is in turn influenced by different factors, such as diet, genotype, age, or sex. We evaluated the effects of breed, 24 h fasting, and dietary energy source (HO: oleic acid versus CH: carbohydrates) on the expression of candidate genes involved in adipogenesis, lipogenesis, and lipolysis in the adipose tissue from Iberian and Duroc growing pigs. The Iberian pigs showed greater feed intake, backfat thickness, and saturated fatty acids (SFA) content in the subcutaneous fat, whereas the Duroc pigs had greater ham weight and polyunsaturated fatty acids (PUFA) content. In both breeds, the diet induced changes in the fatty acid (FA) composition of subcutaneous fat samples. The HO group had higher monounsaturated fatty acids (MUFA) and oleic acid, and lower SFA than the CH group. Regarding gene expression, breed and feeding status (fasting versus postprandial) had significant effects on gene expression, with quantitative interactions between them, while diet showed negligible effects. In general, adipogenic and lipogenic genes were upregulated in the Iberian pigs and in postprandial samples. In contrast, the expression of lipolytic genes showed complex interaction effects. Our results agree with the phenotypic differences between the Iberian and Duroc breeds and with the inhibition of lipogenesis by fasting. Quantitative interactions between breed and feeding status effects were observed, which indicates a different response to fasting of the two breeds, with the obese Iberian breed showing a more stable expression of lipogenic genes. These results highlight the complexity of lipid metabolism regulation, especially in relation to lipolysis processes.

Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing

RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.

The effect of SCD and LEPR genetic polymorphisms on fat content and composition is maintained throughout fattening in Duroc pigs

The effects of the stearoyl-CoA desaturase (SCD; AY487830:g.2228T>C) and leptin receptor (LEPR; NM_001024587:g.1987C>T) polymorphisms on fat content and fatty acid (FA) composition were investigated throughout fattening. Samples of Longissimus thoracis (LT) and subcutaneous fat (SF) from 214 Duroc barrows were collected from 160days to slaughter age (220days) using a longitudinal design. Results indicated that the positive effect of the T allele at the SCD gene on monounsaturated FA and of the T allele at the LEPR gene on saturated FA are maintained throughout the growing-finishing period, both in LT and SF. In LEPR, however, compositional changes, particularly in SF, are a result of increased fatness. There is very limited evidence of genotype by age interaction, and thus it is concluded that the combined selection for the SCD T and LEPR C alleles is a good strategy to increase the MUFA/SFA ratio regardless of the age at slaughter.

Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs

Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.

Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs

The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity.

Early-postnatal changes in adiposity and lipids profile by transgenerational developmental programming in swine with obesity/leptin resistance

Maternal malnutrition during pregnancy, both deficiency and excess, induces changes in the intrauterine environment and the metabolic status of the offspring, playing a key role in the growth, status of fitness/obesity and appearance of metabolic disorders during postnatal life. There is increasing evidence that these effects may not be only limited to the first generation of descendants, the offspring directly exposed to metabolic challenges, but to subsequent generations. This study evaluated, in a swine model of obesity/leptin resistance, the existence and extent of transgenerational developmental programming effects. Pre- and postnatal development, adiposity and metabolic features were assessed in the second generation of piglets, descendant of sows exposed to either undernutrition or overnutrition during pregnancy. The results indicated that these piglets exhibited early-postnatal increases in adiposity and disturbances in lipid profiles compatible with the early prodrome of metabolic syndrome, with liver tissue also displaying evidence of paediatric liver disease. These features indicative of early-life metabolic disorders were more evident in the males that were descended from overfed grandmothers and during the transition from milk to solid feeding. Thus, this study provides evidence supporting transgenerational developmental programming and supports the necessity for the development of strategies for avoiding the current epidemics of childhood overweight and obesity.

Prenatal programming in an obese swine model: sex-related effects of maternal energy restriction on morphology, metabolism and hypothalamic gene expression

Maternal energy restriction during pregnancy predisposes to metabolic alterations in the offspring. The present study was designed to evaluate phenotypic and metabolic consequences following maternal undernutrition in an obese pig model and to define the potential role of hypothalamic gene expression in programming effects. Iberian sows were fed a control or a 50 % restricted diet for the last two-thirds of gestation. Newborns were assessed for body and organ weights, hormonal and metabolic status, and hypothalamic expression of genes implicated in energy homeostasis, glucocorticoid function and methylation. Weight and adiposity were measured in adult littermates. Newborns of the restricted sows were lighter (P <0·01), but brain growth was spared. The plasma concentration of TAG was lower in the restricted newborns than in the control newborns of both the sexes (P <0·01), while the concentration of cortisol was higher in females born to the restricted sows (P <0·04), reflecting a situation of metabolic stress by nutrient insufficiency. A lower hypothalamic expression of anorexigenic peptides (LEPR and POMC, P <0·01 and P <0·04, respectively) was observed in females born to the restricted sows, but no effect was observed in the males. The expression of HSD11B1 gene was down-regulated in the restricted animals (P <0·05), suggesting an adaptive mechanism for reducing the harmful effects of elevated concentrations of cortisol. At 4 and 7 months of age, the restricted females were heavier and fatter than the controls (P< 0·01). Maternal feed restriction induces asymmetrical growth retardation and metabolic alterations in the offspring. Differences in gene expression at birth and higher growth and adiposity in adulthood suggest a female-specific programming effect for a positive energy balance, possibly due to overexposure to endogenous stress-induced glucocorticoids.

Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis

Previous studies on Iberian × Landrace (IBMAP) pig intercrosses have enabled the identification of several quantitative trait locus (QTL) regions related to growth and fatness traits; however, the genetic variation underlying those QTLs are still unknown. These traits are not only relevant because of their impact on economically important production traits, but also because pig constitutes a widely studied animal model for human obesity and obesity-related diseases. The hypothalamus is the main gland regulating growth, food intake, and fat accumulation. Therefore, the aim of this work was to identify genes and/or gene transcripts involved in the determination of growth and fatness in pig by a comparison of the whole hypothalamic transcriptome (RNA-Seq) in two groups of phenotypically divergent IBMAP pigs. Around 16,000 of the ∼25.010 annotated genes were expressed in these hypothalamic samples, with most of them showing intermediate expression levels. Functional analyses supported the key role of the hypothalamus in the regulation of growth, fat accumulation, and energy expenditure. Moreover, 58,927 potentially new isoforms were detected. More than 250 differentially expressed genes and novel transcript isoforms were identified between the two groups of pigs. Twenty-one DE genes/transcripts that colocalized in previously identified QTL regions and/or whose biological functions are related to the traits of interest were explored in more detail. Additionally, the transcription factors potentially regulating these genes and the subjacent networks and pathways were also analyzed. This study allows us to propose strong candidate genes for growth and fatness based on expression patterns, genomic location, and network interactions.

Transcriptional Characterization of Porcine Leptin and Leptin Receptor Genes

The leptin (LEP) and its receptor (LEPR) regulate food intake and energy balance through hypothalamic signaling. However, the LEP-LEPR axis seems to be more complex and its expression regulation has not been well described. In pigs, LEP and LEPR genes have been widely studied due to their relevance. Previous studies reported significant effects of SNPs located in both genes on growth and fatness traits. The aim of this study was to determine the expression profiles of LEP and LEPR across hypothalamic, adipose, hepatic and muscle tissues in Iberian x Landrace backcrossed pigs and to analyze the effects of gene variants on transcript abundance. To our knowledge, non porcine LEPR isoforms have been described rather than LEPRb. A short porcine LEPR isoform (LEPRa), that encodes a protein lacking the intracellular residues responsible of signal transduction, has been identified for the first time. The LEPRb isoform was only quantifiable in hypothalamus while LEPRa appeared widely expressed across tissues, but at higher levels in liver, suggesting that both isoforms would develop different roles. The unique LEP transcript showed expression in backfat and muscle. The effects of gene variants on transcript expression revealed interesting results. The LEPRc.1987C>T polymorphism showed opposite effects on LEPRb and LEPRa hypothalamic expression. In addition, one out of the 16 polymorphisms identified in the LEPR promoter region revealed high differential expression in hepatic LEPRa. These results suggest a LEPR isoform-specific regulation at tissue level. Conversely, non-differential expression of LEP conditional on the analyzed polymorphisms could be detected, indicating that its regulation is likely affected by other mechanisms rather than gene sequence variants. The present study has allowed a transcriptional characterization of LEP and LEPR isoforms on a range of tissues. Their expression patterns seem to indicate that both molecules develop peripheral roles apart from their known hypothalamic signal transduction function.

Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip

BACKGROUND

The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses.

RESULTS

Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes.

CONCLUSIONS

The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.

Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits

Leptin signalling plays a fundamental role in growth, fatness and body composition. The aim of this study was to investigate the porcine LEP gene sequence in an Iberian × Landrace experimental cross to identify polymorphisms associated with productivity and quality traits. Because of the documented effects on these traits of the LEPR c.1987C>T polymorphism, the LEP and LEPR c.1987C>T polymorphisms and their interactions have been jointly investigated. The LEP gene sequencing has allowed the identification of 39 polymorphisms, eight of which are novel. Three intronic SNPs, LEP g.1382C>T, LEP g.1387C>T and LEP g.1723A>G, have been genotyped, and association analyses have been carried out. Analyses of LEP g.1387C>T, fully linked to LEP g.1382C>T, have revealed additive effects on live and carcass weights and dominant effects on several backfat thickness measurements. Novel effects of both LEP and LEPR polymorphisms on fatty acid composition in subcutaneous fat have been detected, probably mediated through the effects on fatness. The results reported here suggest that the T alleles of both LEP g.1387C>T and LEPR c.1987C>T, which are fixed in the Iberian pigs, would lead to an increase in growth, fatness and saturated fatty acid content in fat, which could be explained by an increased feed intake.

Reproductive, endocrine and metabolic feto-maternal features and placental gene expression in a swine breed with obesity/leptin resistance

The current study was conducted in a swine breed (Iberian pig) with a genotype that predisposed the pig to obesity. The aim of the study was to determine the morphological, metabolomic and endocrine features of early conceptuses and to elucidate how placental gene expression (related to placentation, angiogenesis and fetal nutrition), maternal hormones and the metabolome affect the fetal environment and fetal growth. Conceptus viability and growth were found to be related to maternal endocrine (plasma progesterone levels) and metabolic features (plasma levels of leptin, cholesterol, HDL-c, LDL-c and triglycerides). These features were related to the placental expression of the vascular endothelial growth factor A (VEGFA) and leptin (LEP) genes, the placental efficiency and, thus, the nutrition and the metabolism of the fetus (availability of glucose, triglycerides and cholesterol, as HDL-c). Viability of conceptuses in females with evidence of dyslipidemia (low plasma levels of total cholesterol due to low HDL-c concentration but high levels of triglycerides) was diminished. The availability of nutrients and metabolic substrates to the conceptus was also affected in females with higher fat deposition and evidence of dyslipidemia. In conclusion, the conceptus viability and growth appear to be strongly related to maternal metabolic features and, thus, affected in females with alterations in lipid metabolism.

Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data

Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content.

Recombination rates across porcine autosomes inferred from high-density linkage maps

Studies of the variation in recombination rate across the genome provide a better understanding of evolutionary genomics and are also an important step towards mapping and dissecting complex traits in domestic animals. With the recent completion of the porcine genome sequence and the availability of a high-density porcine single nucleotide polymorphism (SNP) array, it is now possible to construct a high-density porcine linkage map and estimate recombination rate across the genome. A total of 416 animals were genotyped with the Porcine SNP60BeadChip, and high-density chromosome linkage maps were constructed using CRI-MAP, assuming the physical order of the Sscrofa10 assembly. The total linkage map length was 2018.79 cM, using 658 meioses and 14,503 SNPs. The estimated average recombination rate across the porcine autosomes was 0.86 cM/Mb. However, a large variation in recombination rate was observed among chromosomes. The estimated average recombination rates (cM/Mb) per chromosome ranged from 0.48 in SSC1 to 1.48 in SSC10, displaying a significant negative correlation with the chromosome sizes. In addition, the analysis of the variation in the recombination rates taking 1-Mb sliding windows has allowed us to demonstrate the variation in recombination rates within chromosomes. In general, a larger recombination rate was observed in the extremes than in the centre of the chromosome. Finally, the ratio between female and male recombination rates was also inferred, obtaining a value of 1.38, with the heterogametic sex having the least recombination.

Endurance exercise is a leptin signaling mimetic in hypothalamus of Wistar rats

BACKGROUND

Endurance exercise is known to promote a substantial effect on the energy balance in rats and humans. However, little is known about the exact mechanisms for the appetite-suppressive effects of endurance exercise. We hypothesized that endurance training might activate signaling cascades in the hypothalamus known to be involved in leptin signaling.

METHODS

16 male Wistar rats were randomly assigned to two groups: sedentary (n = 8) and exercise groups (n = 8). Animals in the exercise group started treadmill running at 30 m/min, 0% grade, for 1 min/bout. Running time was gradually increased by 2 min/bout every day. The training plan was one bout per day during initial two weeks, and two bouts per day during 3rd-9th week. At the end of nine-week experiment, blood was analyzed for low-density lipoprotein cholesterol (LDL-C), triglyceride (TG), total cholesterol (TC), free fatty acid (FFA), interleukin (IL)-6, and leptin in both groups. Activations of janus kinase 2-signaling transducer and activator of transcription 3 (JAK2-STAT3), protein kinase B (Akt), extracellular regulated kninase (ERKs), and suppressor of cytokine signaling 3 (SOCS3) in hypothalamus were measured in the end of nine weeks of exercise protocol.

RESULTS

Nine-week endurance exercise induced lower concentrations of LDL-C, TG, TC, FFA, and leptin in rats (P < 0.05 or P < 0.01). Nine-week endurance exercise significantly increased the circulating IL-6 concentration compared with sedentary group (239.6 ± 37.2 pg/ml vs. 151.8 ± 31.5 pg/ml, P < 0.01). Exercise rats showed significant increases in JAK2, STAT3, Akt, ERKs, and SOCS3 phosphorylations compared with sedentary rats (P < 0.01).

CONCLUSION

The data suggest that endurance exercise is a leptin signaling mimetic in hypothalamus of Wistar rats.

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 6

This study was carried out to identify SNP associated with fatness traits on pig chromosome 6. In total, 11,067 putative genomic variations were detected in 125 complete bacterial artificial chromosome sequences corresponding to the region between SW2098 and SW1881, which harbors multiple QTL affecting intramuscular fat content (IMF) and backfat thickness (BFT). Among 173 putative SNP validated by MassArray, 120 SNP were used in an association study on 541 offspring produced by a cross of Korean native pig and Landrace breeds. The significance level of each SNP was determined using single marker regression analysis. Further, significant threshold values were determined using a false discovery rate. Nine out of 120 SNP showed significant effects on BFT or IMF or both. Of the 9 significant SNP, 4 were significantly associated with IMF, 7 were significantly related to BFT, and 2 SNP (Kps8172 and Kps6413) showed significant effects on both traits. Moreover, multiple regression analysis considering all significant SNP was used to correct spurious false positives due to linkage disequilibrium. Consequently, only 1 SNP (Kps6413) was significant for IMF, whereas 4 SNP including Kps6413 showed significant effects on BFT. The significant SNP had generally additive effects and on average explained 1.72% of the genetic variation for IMF and 3.92% for BFT, respectively. These markers can potentially be applied in pig breeding programs for improving IMF and BFT traits after validation in other populations.

Developmental competence of antral follicles and their oocytes after gonadotrophin treatment of sows with gene polymorphisms for leptin and melanocortin receptors (Iberian pig)

PURPOSE

To evaluate possible differences in follicle and oocyte developmental competence after gonadotrophin treatment in sows of obese and lean genotypes.

METHODS

Follicle dynamics, ovulation rate and oocyte developmental competence to embryo were compared between females, of obese (n = 7) and lean genotypes (n = 10), treated with 1,250 I.U. of eCG and 500 I.U. of hCG.

RESULTS

The obese genotype showed lower numbers of follicles growing to preovulatory stages (12.4 ± 1.8 vs 18.6 ± 1.0, P < 0.05), of corpora lutea (16.0 ± 0.9 vs 23.5 ± 0.9, P < 0.05), and of recovered oocytes/embryos (8.0 ± 1.3 vs 12.9 ± 0.9, P < 0.05). Thereafter, embryo viability rates also decreased when compared to lean genotypes (62.5 vs 77.6%, P < 0.05).

DISCUSSION

To our knowledge, this is the first study analyzing the effect of obese genotypes on the ovarian response to exogenous gonadotrophins in a non-rodent animal model, the pig. A lower efficiency of gonadotrophin treatments for stimulation of follicle development and induction of ovulation was observed.