Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low- (LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.NEW & NOTEWORTHY The duodenum is a key organ for the hunger/satiety loop and nutrient sensing. We investigated how the duodenum transcriptome and DNA methylation profiles are affected by feed intakes in pigs. We observed thousands of changes in gene expression levels between overnight-fasted and fed pigs in high-feed efficiency pig lines, but almost none in the related low-feed efficiency pig line.

Livestock species as emerging models for genomic imprinting

Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.

Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine

BACKGROUND

Heat stress (HS) is an increasing threat for pig production with a wide range of impacts. When submitted to high temperatures, pigs will use a variety of strategies to alleviate the effect of HS. While systemic adaptations are well known, tissue-specific changes remain poorly understood. In this study, thirty-two pigs were submitted to a 5-day HS at 32 °C.

RESULTS

Transcriptomic and metabolomic analyses were performed on several tissues. The results revealed differentially expressed genes and metabolites in different tissues. Specifically, 481, 1774, 71, 1572, 17, 164, and 169 genes were differentially expressed in muscle, adipose tissue, liver, blood, thyroid, pituitary, and adrenal glands, respectively. Regulatory glands (pituitary, thyroid, and adrenal) had a lower number of regulated genes, perhaps indicating an earlier sensitivity to HS. In addition, 7, 8, 2, and 8 metabolites were differentially produced in muscle, liver, plasma, and urine, respectively. The study also focused on the oxidative stress pathway in muscle and liver by performing a correlation analysis between genes and metabolites.

CONCLUSIONS

This study has identified various adaptation mechanisms in swine that enable them to cope with heat stress (HS). These mechanisms include a global decrease in energetic metabolism, as well as changes in metabolic precursors that are linked with protein and lipid catabolism and anabolism. Notably, the adaptation mechanisms differ significantly between regulatory (pituitary, thyroid and adrenal glands) and effector tissues (muscle, adipose tissue, liver and blood). Our findings provide new insights into the comprehension of HS adaptation mechanisms in swine.

A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

BACKGROUND

Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes.

METHODS

We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence.

RESULTS

French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others).

CONCLUSIONS

These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.

Genome‐wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub‐species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the “hybrid” status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 “outliers” (3.6%), for which the proportion of the genome of “domestic” origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of “wild” origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.

Genotyping data of French wild boar populations using porcine genome-wide genotyping array

Objective

The admixture of domestic pig into wild boar populations is controlled until now, by cytogenetic analysis. Even if a first-generation hybrid animal is discernable because of its 37-chromosome karyotype, the cytogenetic method is not applicable in the case of advanced intercrosses. The aim of this study is therefore to evaluate the use of SNP (Single Nucleotide Polymorphism) markers as an alternative technology to characterize recent or past hybridization between the two sub-species. The final goal would be to develop a molecular diagnostic tool.

Data description

The Geneseek Genomic Profiler High-Density porcine beadchip (GGP70KHD, Illumina, USA), comprising 68,516 porcine SNPs, was used on a set of 362 wild boars with diverse chromosomal statuses collected from different areas and breeding environments in France. We generated approximately 62,192–64,046 genotypes per wild boar. The present dataset might be useful for the community (i) for developing molecular tools to evaluate the admixture of domestic pig into wild boar populations, and (ii) for genetic diversity studies including wild boar species or phylogeny analyses of Suidae populations.

Raw data files and a processed matrix data file were deposited in the ArrayExpress at European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) data portal under accession number E-MTAB-10591.

A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities

Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.

Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 2: muscle traits and sensory quality of dry-cured ham

The quality of pork products from local breeds in extensive systems depends, among other things, on pig production. In particular, the variability in climatic conditions and feeding resources may influence the properties of tissues at slaughter and the quality of pork and processed products. The present study (part 2) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin "Noir de Bigorre", castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months and ca. 170 kg BW. Three finishing seasons were considered: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate the specific effects of season on quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. Compared to Winter pigs, Spring and Autumn pigs had higher ultimate pH in the semimembranosus and gluteus medius (GM) muscles, lower meat lightness (P < 0.05) and tended to have higher GM intramuscular fat (IMF) content (P < 0.10). They also had higher GM contents of saturated, monounsaturated and polyunsaturated fatty acids (FAs) than Winter pigs (P < 0.05). Spring pigs had the lowest n-6:n-3 polyunsaturated FA ratio and the highest GM α-tocopherol content (P < 0.001), indicating pig grazing. The finishing season did not influence the processing yield of dry-cured hams (24-month process). Within each seasonal group, ten hams selected for genetic variability and IMF content were analyzed by a trained sensory panel. The season did not modify the appearance or odor, but influenced texture and taste. Hams from Winter and Spring pigs had higher tenderness and melting fat scores than hams from Autumn pigs (P < 0.01). Hams from Spring pigs had higher taste intensity and salty taste (P < 0.01) but lower positive tastes (e.g. fruits, forest) than hams from the other groups. Overall, finishing season had moderate effects on ham sensory traits. Furthermore, our results reveal high redness, tenderness, taste and odor intensity, and low rancid flavor of hams from Gascon pigs produced in an extensive system.

Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 1: Carcass traits and quality of fresh loin

Consumers perceive pork products from local breeds reared in extensive systems positively because of their specific quality properties and regional identity. The sensory, nutritional and technological qualities of these products depend, among other things, on pig production, especially its climatic conditions and the availability of feed resources, which can influence traits of muscle and fat tissue. The present study (part 1) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin "Noir de Bigorre", castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months of age and ca. 170 kg live weight. Three finishing seasons were considered as follows: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate specific effects of season on productive and quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. The finishing season did not influence growth rate. Compared to Winter pigs, Spring and Autumn pigs had slightly lower carcass fatness (P < 0.05), higher ultimate pH and redder and darker color of the Longissimus muscle (LM) (P < 0.01). Loin drip loss was low overall, but was higher for Spring pigs, whereas cooking loss and shear force were similar among seasons. Spring pigs tended to have the lowest LM lipid content, whereas LM myoglobin content remained unaffected. Autumn pigs had lower potential of lipid oxidation in LM than Winter and Spring pigs (P < 0.01), but muscle metabolic traits assessed via glycolytic and oxidative enzyme activities did not differ among seasons. The finishing season modified the backfat fatty acid (FA) profile, with a lower polyunsaturated FA percentage in Autumn pigs than Winter or Spring pigs (P < 0.001), even though the saturated and monounsaturated FA percentages did not differ. In particular, Spring pigs had the lowest n-6:n-3 and C18:2:C18:3 ratios (P < 0.001), as a result of grazing. Overall, Spring and Autumn finishing seasons seem more favorable to technological and sensory pork attributes, with an additional positive effect of Spring finishing on pork nutritional value.

Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency

BACKGROUND

Feed efficiency is a major driver of the sustainability of pig production systems. Understanding the biological mechanisms that underlie these agronomic traits is an important issue for environment questions and farms' economy. This study aimed at identifying genomic regions that affect residual feed intake (RFI) and other production traits in two pig lines divergently selected for RFI during nine generations (LRFI, low RFI; HRFI, high RFI).

RESULTS

We built a whole dataset of 570,447 single nucleotide polymorphisms (SNPs) in 2426 pigs with records for 24 production traits after both imputation and prediction of genotypes using pedigree information. Genome-wide association studies (GWAS) were performed including both lines (global-GWAS) or each line independently (LRFI-GWAS and HRFI-GWAS). Forty-five chromosomal regions were detected in the global-GWAS, whereas 28 and 42 regions were detected in the HRFI-GWAS and LRFI-GWAS, respectively. Among these 45 regions, only 13 were shared between at least two analyses, and only one was common between the three GWAS but it affects different traits. Among the five quantitative trait loci (QTL) detected for RFI, two were close to QTL for meat quality traits and two pinpointed novel genomic regions that harbor candidate genes involved in cell proliferation and differentiation processes of gastrointestinal tissues or in lipid metabolism-related signaling pathways. In most cases, different QTL regions were detected between the three designs, which suggests a strong impact of the dataset structure on the detection power and could be due to the changes in allelic frequencies during the establishment of lines.

CONCLUSIONS

In addition to efficiently detecting known and new QTL regions for feed efficiency, the combination of GWAS carried out per line or simultaneously using all individuals highlighted chromosomal regions that affect production traits and presented significant changes in allelic frequencies across generations. Further analyses are needed to estimate whether these regions correspond to traces of selection or result from genetic drift.

Genetic relationships between feed efficiency and gut microbiome in pig lines selected for residual feed intake

This study aimed to evaluate the genetic relationship between faecal microbial composition and five feed efficiency (FE) and production traits, residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (DFI), average daily gain (ADG) and backfat thickness (BFT). A total of 588 samples from two experimental pig lines developed by divergent selection for RFI were sequenced for the 16 rRNA hypervariable V3‐V4 region. The 75 genera with less than 20% zero values (97% of the counts) and two α‐diversity indexes were analysed. Line comparison of the microbiota traits and estimations of heritability (h²) and genetic correlations (r_g) were analysed. A non‐metric multidimensional scaling showed line differences between genera. The α‐diversity indexes were higher in the LRFI line than in the HRFI line (p < .01), with h² estimates of 0.19 ± 0.08 (Shannon) and 0.12 ± 0.06 (Simpson). Forty‐eight genera had a significant h² (>0.125). The r_g of the α‐diversities indexes with production traits were negative. Some r_g of genera belonging to the Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Lactobacillaceae, Streptococcaceae, Rikenellaceae and Desulfovibrionaceae families significantly differed from zero (p < .05) with FE traits, RFI (3), DFI (7) and BFT (11). These results suggest that a sizable part of the variability of the gut microbial community is under genetic control and has genetic relationships with FE, including diversity indicators. It offers promising perspectives for selection for feed efficiency using gut microbiome composition in pigs.

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

The impact of training on data from genetically-related lines on the accuracy of genomic predictions for feed efficiency traits in pigs

Background

Most genomic predictions use a unique population that is split into a training and a validation set. However, genomic prediction using genetically heterogeneous training sets could provide more flexibility when constructing the training sets in small populations. The aim of our study was to investigate the potential of genomic prediction of feed efficiency related traits using training sets that combine animals from two different, but genetically-related lines. We compared realized prediction accuracy and prediction bias for different training set compositions for five production traits.

Results

Genomic breeding values (GEBV) were predicted using the single-step genomic best linear unbiased prediction method in six scenarios applied iteratively to two genetically-related lines (i.e. 12 scenarios). The objective for all scenarios was to predict GEBV of pigs in the last three generations (~ 400 pigs, G7 to G9) of a given line. For each line, a control scenario was set up with a training set that included only animals from that line (target line). For all traits, adding more animals from the other line to the training set did not increase prediction accuracy compared to the control scenario. A small decrease in prediction accuracies was found for average daily gain, backfat thickness, and daily feed intake as the number of animals from the target line decreased in the training set. Including more animals from the other line did not decrease prediction accuracy for feed conversion ratio and residual feed intake, which were both highly affected by selection within lines. However, prediction biases were systematic for these cases and might be reduced with bivariate analyses.

Conclusions

Our results show that genomic prediction using a training set that includes animals from genetically-related lines can be as accurate as genomic prediction using a training set from the target population. With combined reference sets, accuracy increased for traits that were highly affected by selection. Our results provide insights into the design of reference populations, especially to initiate genomic selection in small-sized lines, for which the number of historical samples is small and that are developed simultaneously. This applies especially to poultry and pig breeding and to other crossbreeding schemes.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Background

Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H_P) and fixation index (F_ST)] and group-based F_ST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Results

We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.

Conclusions

Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Effect of chronic and acute heat challenges on fecal microbiota composition, production, and thermoregulation traits in growing pigs1,2

The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F_ST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Genotype by environment interactions for performance and thermoregulation responses in growing pigs1,2

Heat stress affects pig health, welfare, and production, and thus the economic viability of the pig sector in many countries. Breeding for heat tolerance is a complex issue, increasingly important due to climate change and the development of pig production in tropical areas. Characterizing genetic determinism of heat tolerance would help building selection schemes dedicated to high performance in tropical areas. The main objective of our study was to estimate the genetic parameters for production and thermoregulation traits in two highly related growing pig populations reared in temperate (TEMP) or tropical humid (TROP) environment. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. Phenotypic data were obtained on a total of 1,297 pigs using the same procedures in both environments, for body weight (BW, at weeks 11 and 23), daily feed intake (ADFI), backfat thickness (BFT, at weeks 19 and 23), cutaneous temperature (CT, at weeks 19 and 23), and rectal temperature (RT, at weeks 19, 21, and 23). Feed conversion ratio (FCR) and residual feed intake (RFI) were computed for the whole test period (11 to 23 wk). Criteria comparing the fits to the data revealed genotype × environment (G × E) interactions for most traits but not for FCR. The variance components were obtained using two different methods, a restricted maximum likelihood method and a Bayesian Markov chain Monte Carlo method, considering that traits are either similar or different in each environment. Regardless of the method, heritability estimates for production traits were moderate to high, except for FCR (lower than 0.18). Heritability estimates for RT were low to moderate, ranging from 0.04 to 0.34. The genetic correlations of each trait between environments generally differed from 1, except for FCR and ADG. For most thermoregulation traits, they also did not differ significantly from zero, suggesting that the main genetic bases of heat tolerance may vary in different environment. Within environments, the unfavorable genetic correlations between production traits and RT suggest an antagonism between the ability to maintain inner temperature and the ability to increase ADFI and ADG. However, greater RT were also associated to leaner pigs and better feed efficiency. Nevertheless, due to large inaccuracies of these estimations, larger cohorts would be needed to decide about the best breeding schemes to choose for tropical pig production.

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.

New Insights into the Melanophilin (MLPH) Gene Affecting Coat Color Dilution in Rabbits

Coat color dilution corresponds to a specific pigmentation phenotype that leads to a dilution of wild type pigments. It affects both eumelanin and pheomelanin containing melanosomes. The mode of inheritance of the dilution phenotype is autosomal recessive. Candidate gene approaches focused on the melanophilin (MLPH) gene highlighted two variants associated with the dilution phenotype in rabbits: The c.111-5C>A variant that is located in an acceptor splice site or the c.585delG variant, a frameshift mutation. On the transcript level, the skipping of two exons has been reported as the molecular mechanism responsible for the coat color dilution. To clarify, which of the two variants represents the causal variant, (i) we analyzed their allelic segregation by genotyping Castor and Chinchilla populations, and (ii) we evaluated their functional effects on the stability of MLPH transcripts in skin samples of animals with diluted or wild type coat color. Firstly, we showed that the c.585delG variant showed perfect association with the dilution phenotype in contrast to the intronic c.111-5C>A variant. Secondly, we identified three different MLPH isoforms including the wild type isoform, the exon-skipping isoform and a retained intron isoform. Thirdly, we observed a drastic and significant decrease of MLPH transcript levels in rabbits with a coat color dilution (p-values ranging from 10⁻⁰³ to 10⁻⁰⁶). Together, our results bring new insights into the coat color dilution trait.

1HNMR-Based metabolomic profiling method to develop plasma biomarkers for sensitivity to chronic heat stress in growing pigs

The negative impact of heat stress (HS) on the production performances in pig faming is of particular concern. Novel diagnostic methods are needed to predict the robustness of pigs to HS. Our study aimed to assess the reliability of blood metabolome to predict the sensitivity to chronic HS of 10 F1 (Large White × Creole) sire families (SF) reared in temperate (TEMP) and in tropical (TROP) regions (n = 56±5 offsprings/region/SF). Live body weight (BW) and rectal temperature (RT) were recorded at 23 weeks of age. Average daily feed intake (AFDI) and average daily gain were calculated from weeks 11 to 23 of age, together with feed conversion ratio. Plasma blood metabolome profiles were obtained by Nuclear Magnetic Resonance spectroscopy (^1HNMR) from blood samples collected at week 23 in TEMP. The sensitivity to hot climatic conditions of each SF was estimated by computing a composite index of sensitivity (I_sens) derived from a linear combination of t statistics applied to familial BW, ADFI and RT in TEMP and TROP climates. A model of prediction of sensitivity was established with sparse Partial Least Square Discriminant Analysis (sPLS-DA) between the two most robust SF (n = 102) and the two most sensitive ones (n = 121) using individual metabolomic profiles measured in TEMP. The sPLS-DA selected 29 buckets that enabled 78% of prediction accuracy by cross-validation. On the basis of this training, we predicted the proportion of sensitive pigs within the 6 remaining families (n = 337). This proportion was defined as the predicted membership of families to the sensitive category. The positive correlation between this proportion and I_sens (r = 0.97, P < 0.01) suggests that plasma metabolome can be used to predict the sensitivity of pigs to hot climate.

Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing

Reciprocal translocations are the most frequently occurring constitutional structural rearrangements in mammalian genomes. In phenotypically normal pigs, an incidence of 1/200 is estimated for such rearrangements. Even if constitutional translocations do not necessarily induce defects and diseases, they are responsible for significant economic losses in domestic animals due to reproduction failures. Over the last 30 years, advances in molecular and cytogenetic technologies have led to major improvements in the resolution of the characterization of translocation events. Characterization of translocation breakpoints helps to decipher the mechanisms that lead to such rearrangements and the functions of the genes that are involved in the translocation. Here, we describe the fine characterization of a reciprocal translocation t(3;4) (p1.3;q1.5) detected in a pig line. The breakpoint was identified at the base-pair level using a positional cloning and chromosome walking strategy in somatic cell hybrids that were generated from an animal that carries this translocation. We show that this translocation occurs within the ADAMTSL4 gene and results in a loss of expression in homozygous carriers. In addition, by taking this translocation as a model, we used a whole-genome next-generation mate-pair sequencing approach on pooled individuals to evaluate this strategy for high-throughput screening of structural rearrangements.

Interactions between sire family and production environment (temperate vs. tropical) on performance and thermoregulation responses in growing pigs

The aim of this study was to evaluate the effect of 2 climatic environments (temperate [TEMP] vs. tropical humid [TROP]) on production and thermoregulation traits in growing pigs. A backcross design involving Large White (LW; heat sensitive) and Creole (CR; heat tolerant) pigs was studied. The same 10 F LW × CR boars were mated with related LW sows in each environment. A total of 1,298 backcross pigs ( = 634 pigs from 11 batches for the TEMP environment and = 664 pigs from 12 batches for the TROP environment) were phenotyped on BW (every 15 d from wk 11 to 23 of age), voluntary feed intake (ADFI, from wk 11 to 23), backfat thickness (BFT; at wk 19 and 23), skin temperature (ST; at wk 19 and 23), and rectal temperature (RT; at wk 19, 21, and 23). The feed conversion ratio was computed for the whole test period (11 to 23 wk). The calculation of the temperature-humidity index showed an average difference of 2.4°C between the TEMP and TROP environments. The ADG and ADFI were higher in the TEMP environment than in the TROP environment (834 vs. 754 g/d and 2.20 vs. 1.80 kg/d, respectively; < 0.001). Body temperatures were higher in the TROP environment than in the TEMP environment (35.9 vs. 34.8°C for ST and 39.5 vs. 39.3°C for RT, respectively; < 0.001). Most of the studied traits (i.e., BW, BFT, ADG, ADFI, and RT) were affected by sire family × environment interactions ( < 0.05), resulting in "robust" and "sensitive" families. Our results show a family dependency in the relationships between heat resistance and robustness, suggesting the possibility of finding genotypes with high production and low heat sensitivity. Further research is needed to confirm the genetic × environment interaction and to detect QTL related to heat tolerance.

Review: divergent selection for residual feed intake in the growing pig

This review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant (P<0.001) line differences for RFI (-165 g/day in the low RFI (LRFI) line compared with high RFI line) and daily feed intake (-270 g/day). Low responses were observed on growth rate (-12.8 g/day, P<0.05) and body composition (+0.9 mm backfat thickness, P=0.57; -2.64% lean meat content, P<0.001) with a marked response on feed conversion ratio (-0.32 kg feed/kg gain, P<0.001). Reduced ultimate pH and increased lightness of the meat (P<0.001) were observed in LRFI pigs with minor impact on the sensory quality of the meat. These changes in meat quality were associated with changes of the muscular energy metabolism. Reduced maintenance energy requirements (-10% after five generations of selection) and activity (-21% of time standing after six generations of selection) of LRFI pigs greatly contributed to the gain in energy efficiency. However, the impact of selection for RFI on the protein metabolism of the pig remains unclear. Digestibility of energy and nutrients was not affected by selection, neither for pigs fed conventional diets nor for pigs fed high-fibre diets. A significant improvement of digestive efficiency could likely be achieved by selecting pigs on fibre diets. No convincing genetic or blood biomarker has been identified for explaining the differences in RFI, suggesting that pigs have various ways to achieve an efficient use of feed. No deleterious impact of the selection on the sow reproduction performance was observed. The resource allocation theory states that low RFI may reduce the ability to cope with stressors, via the reduction of a buffer compartment dedicated to responses to stress. None of the experiments focussed on the response of pigs to stress or challenges could confirm this theory. Understanding the relationships between RFI and responses to stress and energy demanding processes, as such immunity and lactation, remains a major challenge for a better understanding of the underlying biological mechanisms of the trait and to reconcile the experimental results with the resource allocation theory.

Expressed alleles of imprinted IGF2, DLK1 and MEG3 colocalize in 3D-preserved nuclei of porcine fetal cells

Background

To explore the relationship between spatial genome organization and gene expression in the interphase nucleus, we used a genomic imprinting model, which offers parental-specific gene expression. Using 3D FISH in porcine fetal liver cells, we compared the nuclear organization of the two parental alleles (expressed or not) of insulin-like growth factor 2 (IGF2), a paternally imprinted gene located on chromosome 2. We investigated whether its nuclear positioning favors specific locus associations. We also tested whether IGF2 is implicated in long-range chromatin trans-associations as previously shown in the mouse model species for its reciprocal imprinted gene H19.

Results

We focused on the 3D position of IGF2 alleles, with respect to their individual chromosome 2 territories. The paternally expressed allele was tagged with nascent RNA. There were no significant differences in the position of the two alleles (p = 0.06). To determine long-range chromatin trans-interactions, we chose 12 genes, some of which are known to be imprinted in mammalian model species and belong to a network of imprinted genes (i.e. SLC38A4, DLK1, MEG3, and ZAC1). We screened them and ABCG2, OSBP2, OSBPL1, RPL32, NF1, ZAR1, SEP15, GPC3 for associations with IGF2 in liver cells. All imprinted genes tested showed an association with IGF2. The DLK1/MEG3 locus showed the highest rate of colocalization. This gene association was confirmed by 3D FISH (in 20 % of the nuclei analyzed), revealing also the close proximity of chromosomes 2 and 7 (in 60 % of nuclei). Furthermore, our observations showed that the expressed paternal IGF2 allele is involved in this association. This IGF2-(DLK1/MEG3) association also occurred in a high percentage of fetal muscle cells (36 % of nuclei). Finally, we showed that nascent IGF2, DLK1 and MEG3 RNAs can associate in pairs or in a three-way combination.

Conclusion

Our results show that trans-associations occur between three imprinted genes IGF2, DLK1 and MEG3 both in fetal liver and muscle cells. All three expressed alleles associated in muscle cells. Our findings suggest that the 3D nuclear organization is linked to the transcriptional state of these genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12860-016-0113-9) contains supplementary material, which is available to authorized users.

Transcript levels of genes implicated in steroidogenesis in the testes and fat tissue in relation to androstenone accumulation in fat of pubertal pigs

The present study was performed to measure messenger RNA levels of steroidogenic enzymes in testes and fat tissue and determine whether they are related to fat androstenone level. Real-time polymerase chain reaction experiments were performed on 26 testes and 12 adipose tissue samples from pubertal boars using 21 genes. The absence of significant correlations between fat androstenone and the transcriptional activity of the SRD5A2 and SRD5A3 genes but the high correlation coefficient with that of the SRD5A1 gene (r = 0.62, P < 0.05) suggests that the enzyme coded by SRD5A1 is mainly responsible for the last step of androstenone synthesis. The testicular transcriptional activities of CYP17, CYP11A1, CYP19A, AKR1C-pig6, SRD5A1, LHCGR, and AR were significantly correlated. Only transcriptional levels of CYP17, CYP11A1, CYP19A, SRD5A1, and AKR1C-pig6 were correlated with the fat concentration of androstenone (0.57 < r < 0.70, P < 0.05) confirming that the amount of androstenone stored in fat is related to the production in testes of androstenone and more generally to all sex steroids. Altogether, our data are in favor of a preponderant role of AKR1C-pig6 instead of HSD17B3 for testicular synthesis of steroids. Concerning fat tissue, our data do not support a significant de novo biosynthesis of steroids in porcine adipose tissues. The presence of transcripts coding for steroid enzymes, especially those of AKR1C-pig6, suggests that steroids can be transformed. None of transcript abundance was related to androstenone accumulation (P > 0.1). Therefore, steroids synthesized elsewhere can be transformed in fat tissue but synthesis of androstenone is unlikely.

Pedigree and genomic evaluation of pigs using a terminal-cross model

Background

In crossbreeding schemes, within-line selection of purebreds is performed mainly to improve the performance of crossbred descendants under field conditions. The genetic correlation between purebred and crossbred performance is an important parameter to be assessed because purebred performance can be a poor predictor of the performance of crossbred offspring. With the availability of high-density markers, the feasibility of using crossbred information to evaluate purebred candidates can be reassessed. This study implements and applies a single-step terminal-cross model (GEN) to real data to estimate the genetic parameters of several production and quality traits in pigs.

Methods

Piétrain sires were mated with Piétrain and Large White dams to produce purebred and crossbred male half-sib piglets; growth rate, feed conversion ratio, lean meat, pH of longissimus dorsi muscle, drip loss and intramuscular fat content were recorded on all half-sibs. Animals were genotyped using the Illumina Porcine SNP60 BeadChip. The genetic correlation between purebred and crossbred performance was estimated separately for each trait. Purebred animals were evaluated using an animal model, whereas the additive genetic effect of a crossbred individual was decomposed into the additive effects of the sire and dam and a Mendelian sampling effect that was confounded with the residual effect. Genotypes of the Piétrain animals were integrated in the genetic evaluation by using a single-step procedure. As benchmarks, we used a model that was identical to GEN but only accounted for pedigree information (PED) and also two univariate single-step models (GEN_UNI) that took either purebred or crossbred performance into account.

Results

Genetic correlations between purebred and crossbred performance were high and positive for all traits (>0.69). Accuracies of estimated breeding values of genotyped sires and purebred offspring that were obtained with the GEN model outperformed both those obtained with the PED and the GEN_UNI models. The use of genomic information increased the predictive ability of the GEN model, but it did not substantially outperform the GEN_UNI models.

Conclusions

We present a single-step terminal-cross model that integrates genomic information of purebred and crossbred performance by using available software. It improves the theoretical accuracy of genetic evaluations in breeding programs that are based on crossbreeding.

Exploration of steroidogenesis-related genes in testes, ovaries, adrenals, liver and adipose tissue in pigs

To explore the metabolism of steroids in the pig species, a qualitative PCR analysis was performed for the main transcript of 27 genes involved in steroid metabolism. We compared samples of testes, adipose tissue and liver from immature and peripubertal males, adrenal cortex from peripubertal males, ovaries from cyclic females and adipose tissue from peripubertal females. Some genes were shown to have a tissue-specific expression. Two of them were expressed only in testes, ovaries and adrenals: CYP11A1 and CYP11B. The CYP21 and HSD17B3 genes, were expressed respectively only in adrenals and only in testes. Very few differences were observed between transcriptional patterns of peripubertal testes and adrenal glands as well as between male and female fat tissues. However, the expression of genes involved in the sulfonation of steroids was higher in testes than in adrenals from males. Main differences between ovaries and testes were observed for HSD17B1/2/3, AKR1C-pig6 and sulfotransferase genes (SULT2A1/SULT2B1). The present study shows that the SRD5A2 and CYP21 genes were not involved in the testicular biosynthesis of androstenone. It also shows that porcine adrenal glands produce essentially corticosteroids and that fat tissue is unable to produce de novo steroids.

Genetic parameters for litter size, piglet growth and sow's early growth and body composition in the Chinese-European line Tai Zumu

Genetics of piglet growth in association with sow's early growth and body composition were estimated in the Tai Zumu line. Piglet and sow's litter growth traits were calculated from individual weights collected at birth and at 3 weeks of age. Sow's litter traits included the number of piglets born alive (NBA), the mean piglet weight (MW) and the standard deviation of weights within the litter (SDW). Sow's early growth was measured by the age at 100 kg (A100), and body composition included backfat thickness (BF100). A main objective of this study was to estimate separately the direct genetic effect (d) and the maternal genetic effect (m) on piglet weight and daily weight gain during lactation. Variance components were estimated using the restricted maximum likelihood methodology based on animal models. The heritability estimates were 0.19 for NBA, 0.15 and 0.26 for SDW and MW at 3 weeks and 0.42 and 0.70 for A100 and BF100. The NBA was almost independent from SDW. Conversely, the A100 and BF100 were correlated unfavourably with SDW (rg <-0.24, SE<0.12). A stronger selection for litter size should have little effect on litter homogeneity in weights. Selection for lean growth rate tends to favour heterogeneity in weights. The direct effect on piglet weight at birth and daily weight gain accounted for 12% (h(²) (d) = 0.02) and 50% (h(²) (d) = 0.11) of the genetic variance, respectively. The association between d and m for piglet weight was not different from zero at birth (rg = 0.19, SE = 0.27), but a strong antagonism between d and m for daily weight gain from birth to 3 weeks was found (rg = -0.41, SE = 0.17). Substantial direct and maternal genetic effects influenced piglet growth until weaning in opposite way.

A genome-wide association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs

Among farm animals, pigs are known to show XX sex-reversal. In such cases the individuals are genetically female but exhibit a hermaphroditism, or a male phenotype. While the frequency of this congenital disease is quite low (less than 1%), the economic losses are significant for pig breeders. These losses result from sterility, urogenital infections and the carcasses being downgraded because of the risk of boar taint. It has been clearly demonstrated that the SRY gene is not involved in most cases of sex-reversal in pigs, and that autosomal recessive mutations remain to be discovered. A whole-genome scan analysis was performed in the French Large-White population to identify candidate genes: 38 families comprising the two non-affected parents and 1 to 11 sex-reversed full-sib piglets were genotyped with the PorcineSNP60 BeadChip. A Transmission Disequilibrium Test revealed a highly significant candidate region on SSC12 (most significant p-value<4.65.10^-10) containing the SOX9 gene. SOX9, one of the master genes involved in testis differentiation, was sequenced together with one of its main regulatory region Tesco. However, no causal mutations could be identified in either of the two sequenced regions. Further haplotype analyses did not identify a shared homozygous segment between the affected pigs, suggesting either a lack of power due to the SNP properties of the chip, or a second causative locus. Together with information from humans and mice, this study in pigs adds to the field of knowledge, which will lead to characterization of novel molecular mechanisms regulating sexual differentiation and dysregulation in cases of sex reversal.

Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes

BACKGROUND

Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F₂ populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis.

RESULTS

A female-specific linkage map with an average distance of 2 cM between markers in the initial QTL interval (SW2456-SW1943) was created and used here. The CI of QTL for BFT, HW and LEA were narrowed down to 6-7 cM, resulting from the joint analysis. For IMF, two linked QTL were revealed in the INRA population but not in the JXAU population, causing a wider CI (13 cM) for IMF QTL. Linkage analyses using two subsets of INRA F₁ dam families demonstrate that the BFT and HW QTL were segregating in the Meishan pigs. Moreover, haplotype comparisons between these dams suggest that within the refined QTL region, the recombination coldspot (~34 Mb) flanked by markers MCSE3F14 and UMNP1218 is unlikely to contain QTL genes. Two SNPs in the ACSL4 gene were identified and showed significant association with BFT and HW, but they and the known polymorphisms in the other two genes are unlikely to be causal mutations.

CONCLUSION

The candidate QTL regions have been greatly reduced and the QTL are most likely located downstream of the recombination coldspot. The segregation of SSCX QTL for BFT and HW within Meishan breed provides an opportunity for us to make effective use of Meishan chromosome X in crossbreeding. Further studies should attempt to identify the impact of additional DNA sequence (e.g. CNV) and expression variation in the three genes or their surrounding genes on these traits.

Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs

Background

Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least one additional QTL should segregate downstream of this mutation. A marker-assisted backcrossing design was set up in order to confirm the segregation of this second locus, reduce its confidence interval and better understand its mode of segregation.

Results

Five recombinant full-sibs, with genotype G/G at the IGF2 mutation, were progeny-tested. Only two of them displayed significant QTL for fatness traits although four inherited the same paternal and maternal chromosomes, thus exhibiting the same haplotypic contrast in the QTL region. The hypothesis of an interaction with another region in the genome was proposed to explain these discrepancies and after a genome scan, four different regions were retained as potential interacting regions with the SSC2 QTL. A candidate interacting region on SSC13 was confirmed by the analysis of an F2 pedigree, and in the backcross pedigree one haplotype in this region was found to mask the SSC2 QTL effect.

Conclusions

Assuming the hypothesis of interactions with other chromosomal regions, the QTL could be unambiguously mapped to a 30 cM region delimited by recombination points. The marker-assisted backcrossing design was successfully used to confirm the segregation of a QTL on SSC2 and, because full-sibs that inherited the same alleles from their two parents were analysed, the detection of epistatic interactions could be performed between alleles and not between breeds as usually done with the traditional Line-Cross model. Additional analyses of other recombinant sires should provide more information to further improve the fine-mapping of this locus, and confirm or deny the interaction identified between chromosomes 2 and 13.

Towards candidate genes affecting body fatness at the SSC7 QTL by expression analyses

A quantitative trait locus (QTL) affecting fatness in a way opposite to expectations based on breed means was mapped to swine chromosome 7 (SSC7) using crosses between Large White (LW) and Meishan (MS) founders. Defining the molecular fatness trait more explicitly would allow deducing positional candidate genes, for which expression differences must be analysed in experimental populations. First, mRNA levels of genes representing sequential steps in adipogenesis or involved in lipid metabolism were studied in backfat of pigs having homozygous LW(QTL7)/LW(QTL7) or heterozygous LW(QTL7)/MS(QTL7) alleles and considered at two ages. mRNA level of DLK1 expressed in preadipocytes was greater in MS(QTL7)/LW(QTL7) pigs than in homozygous pigs at 28 days. Transcript abundances of CEBPA involved in differentiation, the prolipogenic FASN gene and the adipocyte-specific marker FABP4 were lower in MS(QTL7)/LW(QTL7) pigs compared with LW(QTL7)/LW(QTL7) pigs at 150 days. Because these results suggest a lag time in terminal differentiation associated with the MS allele, seven genes in the QTL interval were deduced as promising candidates for the QTL effect by bioinformatics analysis. Among them, PPARD and CDKN1A had lower expression levels in MS(QTL7)/LW(QTL7) pigs at both ages. Genotype-related differences were observed in mRNA levels of PPARD target genes involved in cell differentiation (FZD7) or fatty acid oxidation (ACADL and ACOX1) at 150 days. These results re-evaluate the potential of PPARD to explain part of variation in pig adiposity.

Microsatellite mapping of quantitative trait loci affecting female reproductive tract characteristics in Meishan x Large White F(2) pigs

A QTL analysis of female reproductive data from a 3-generation experimental cross between Meishan and Large White pig breeds is presented. Six F(1) boars and 23 F(1) sows, progeny of 6 Large White boars and 6 Meishan sows, produced 502 F(2) gilts whose reproductive tract was collected after slaughter at 30 d of gestation. Five traits [i.e., the total weight of the reproductive tract, of the empty uterine horns, of the ovaries (WOV), and of the embryos], as well as the length of uterine horns (LUH), were measured and analyzed with and without adjustment for litter size. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross regression and a half-full sib maximum likelihood test. A total of 18 genome-wide significant (P < 0.05) QTL were detected on 9 different chromosomes (i.e., SSC 1, 5, 6, 7, 9, 12, 13, 18, and X). Five genome-wide significant QTL were detected for LUH, 4 for weight of the empty uterine horns and WOV, 2 for total weight of the reproductive tract, and 1 for weight of the embryos. Twenty-two additional suggestive QTL were also detected. The largest effects were obtained for LUH and WOV on SSC13 (9.2 and 7.0% of trait phenotypic variance, respectively). Meishan alleles had both positive (e.g., on SSC7) and negative effects (e.g., on SSC13) on the traits investigated. Moreover, the QTL were generally not fixed in founder breeds, and opposite effects were in some cases obtained in different families. Although reproductive tract characteristics had only a moderate correlation with reproductive performances, most of the major QTL detected in this study were previously reported as affecting female reproduction, generally with reduced significance levels. This study thus shows that focusing on traits with high heritability might help to detect loci involved in low heritability major traits for breeding.

New investigations around CYP11A1 and its possible involvement in an androstenone QTL characterised in Large White pigs

BACKGROUND

Previously, in boars with extreme androstenone levels, differential expression of the CYP11A1 gene in the testes has been characterised. CYP11A1 is located in a region where a QTL influencing boar fat androstenone levels has been detected in a Large White pig population. Clarifying the role of CYP11A1 in boar taint is important because it catalyses the initial step of androstenone synthesis and also of steroid synthesis.

RESULTS

A genome-wide association study located CYP11A1 at approximately 1300 kb upstream from SNP H3GA0021967, defining the centre of the region containing the QTL for androstenone variation. In this study, we partially sequenced the CYP11A1 gene and identified several new single nucleotide polymorphisms (SNP) within it. Characterisation of one animal, heterozygous for CYP11A1 testicular expression but homozygous for a haplotype of a large region containing CYP11A1, revealed that variation of CYP11A1 expression is probably regulated by a mutation located downstream from the SNP H3GA0021967. We analysed CYP11A1 expression in LW families according to haplotypes of the QTL region's centre. Effects of haplotypes on CYP11A1 expression and on androstenone accumulation were not concordant.

CONCLUSION

This study shows that testicular expression of CYP11A1 is not solely responsible for the QTL influencing boar fat androstenone levels. As a conclusion, we propose to refute the hypothesis that a single mutation located near the centre of the QTL region could control androstenone accumulation in fat by regulating the CYP11A1 expression.

Expression levels of 25 genes in liver and testis located in a QTL region for androstenone on SSC7q1.2

A quantitative trait locus (QTL) for boar fat androstenone levels has been identified near the SSC7 centromere in a Large White × Meishan cross. Backcrosses were produced to isolate the Chinese haplotype in a European genetic background. The expression of 25 genes from the QTL region was studied in the testes and livers of 5-month-old backcross boars, with the aim of identifying the causal gene. Using Fluidigm, a new high-throughput technology, the expression of 25 genes was measured in a single real-time PCR experiment. This study found six significantly down-regulated genes (C6ORF106, C6ORF81, CLPS, SLC26A8, SRPK1 and MAPK14) in the testes of MS-LW backcross boars. However, according to current knowledge, none of the genes appear to be related to androstenone metabolism. In the livers, none of the genes were significantly up- or down-regulated, including TEAD3, which was previously designated as a possible candidate to explain this QTL.

Number and mode of inheritance of QTL influencing backfat thickness on SSC2p in Sino-European pig pedigrees

Background

In the pig, multiple QTL associated with growth and fatness traits have been mapped to chromosome 2 (SSC2) and among these, at least one shows paternal expression due to the IGF2-intron3-G3072A substitution. Previously published results on the position and imprinting status of this QTL disagree between analyses from French and Dutch F2 crossbred pig populations obtained with the same breeds (Meishan crossed with Large White or Landrace).

Methods

To study the role of paternal and maternal alleles at the IGF2 locus and to test the hypothesis of a second QTL affecting backfat thickness on the short arm of SSC2 (SSC2p), a QTL mapping analysis was carried out on a combined pedigree including both the French and Dutch F2 populations, on the progeny of F1 males that were heterozygous (A/G) and homozygous (G/G) at the IGF2 locus. Simulations were performed to clarify the relations between the two QTL and to understand to what extent they can explain the discrepancies previously reported.

Results

The QTL analyses showed the segregation of at least two QTL on chromosome 2 in both pedigrees, i.e. the IGF2 locus and a second QTL segregating at least in the G/G F1 males and located between positions 30 and 51 cM. Statistical analyses highlighted that the maternally inherited allele at the IGF2 locus had a significant effect but simulation studies showed that this is probably a spurious effect due to the segregation of the second QTL.

Conclusions

Our results show that two QTL on SSC2p affect backfat thickness. Differences in the pedigree structures and in the number of heterozygous females at the IGF2 locus result in different imprinting statuses in the two pedigrees studied. The spurious effect observed when a maternally allele is present at the IGF2 locus, is in fact due to the presence of a second closely located QTL. This work confirms that pig chromosome 2 is a major region associated with fattening traits.

A locally congenic backcross design in pig: a new regional fine QTL mapping approach miming congenic strains used in mouse

BACKGROUND

In previous studies, a major QTL affecting fatness and growth has been mapped to pig chromosome 1q (SSC1q) using Large White - Meishan intercrosses. A higher fat depth and a larger growth rate have been reported for the allele of MS origin. Additionally the LW allele showed partial dominance effects over the MS allele for both traits. In order to refine the QTL mapping interval, advanced backcross generations were produced. Recombinant heterozygous sires were mated to LW sows in order to progeny test the sire segregation of the QTL and refine the QTL localisation. However due to the partial dominance of the LW allele, BC scheme using LW as the receiving population was not optimal.

RESULTS

To overcome the difficulties related to the dominance of the LW QTL allele, a population of dams locally homozygous for the MS haplotype in the QTL region, but with an overall 29/32 LW genetic background, has been set up. Progeny testing results, using these receiver dams, were much more significant than those previously obtained with LW dams, and the SSC1 QTL interval was refined to 8 cM. Considering the results obtained, a powerful experimental design for farm animals is proposed, mimicking locally genetically identical strains used in mouse for QTL fine mapping.

CONCLUSIONS

We have further characterized the fatness QTL on pig chromosome 1 and refined its map position from a 30 cM interval to a 8 cM interval, using a locally congenic BC design. We have obtained highly significant results and overcome difficulties due to the dominance of the LW allele. This design will be used to produce additional, advanced BC families to further refine this QTL localization.

Meiotic studies of a 38,XY/39,XXY mosaic boar

Klinefelter's syndrome (KS) is the most common sex chromosome abnormality identified in human males. This syndrome is generally associated with infertility. Men with KS may have a 47,XXY or a 46,XY/47,XXY karyotype. Studies carried out in humans and mice suggest that only XY cells are able to enter and complete meiosis. These cells could originate from the XY cells present in mosaic patients or from XXY cells that have lost one X chromosome. In pig, only 3 cases of pure 39,XXY have been reported until now, and no meiotic analysis was carried out. For the first time in pig species we report the analysis of a 38,XY/39,XXY boar and describe the origin of the supplementary X chromosome and the chromosomal constitutions of the germ and Sertoli cells.

Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6

Background

In pig, a number of experiments have been set up to identify QTL and a multitude of chromosomal regions harbouring genes influencing traits of interest have been identified. However, the mapping resolution remains limited in most cases and the detected QTL are rather inaccurately located. Mapping accuracy can be improved by increasing the number of phenotyped and genotyped individuals and/or the number of informative markers. An alternative approach to overcome the limited power of individual studies is to combine data from two or more independent designs.

Methods

In the present study we report a combined analysis of two independent design (a French and a Dutch F2 experimental designs), with 2000 F2 individuals. The purpose was to further map QTL for growth and fatness on pig chromosomes 2, 4 and 6. Using QTL-map software, uni- and multiple-QTL detection analyses were applied separately on the two pedigrees and then on the combination of the two pedigrees.

Results

Joint analyses of the combined pedigree provided (1) greater significance of shared QTL, (2) exclusion of false suggestive QTL and (3) greater mapping precision for shared QTL.

Conclusions

Combining two Meishan x European breeds F2 pedigrees improved the mapping of QTL compared to analysing pedigrees separately. Our work was facilitated by the access to raw phenotypic data and DNA of animals from both pedigrees and the combination of the two designs with the addition of new markers allowed us to fine map QTL without phenotyping additional animals.

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

BACKGROUND

Variations in recombination fraction (theta) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White male symbol x Chinese Meishan female symbol, and White Duroc male symbol x Chinese Erhualian female symbol), we were able to evaluate the heterogeneity in theta for a specific interval among individual F1 females.

RESULTS

Alignments between the cytogenetic map, radiation hybrid (RH) map, genetic maps and clone map of SSC-X with the physical map of human chromosome X (HSA-X) are presented. The most likely order of 60 markers on SSC-X is inferred. The average recombination rate across SSC-X is of approximately 1.27 cM/Mb. However, almost no recombination occurred in a large region of approximately 31 Mb extending from the centromere to Xq21, whereas in the surrounding regions and in the Xq telomeric region a recombination rate of 2.8-3.3 cM/Mb was observed, more than twice the chromosome-wide average rate. Significant differences in theta among F1 females within each population were observed for several chromosomal intervals. The largest variation was observed in both populations in the interval UMNP71-SW1943, or more precisely in the subinterval UMNP891-UMNP93. The individual variation in theta over this subinterval was found associated with F1 females' maternal haplotypes (Chinese pig haplotypes) and independent of paternal haplotype (European pig haplotypes). The theta between UMNP891 and UMNP93 for haplotype 1122 and 4311 differed by more than fourteen-fold (10.3% vs. 0.7%).

CONCLUSIONS

This study reveals marked regional, individual and haplotype-specific differences in recombination rate on SSC-X. Lack of recombination in such a large region makes it impossible to narrow QTL interval using traditional fine-mapping approaches. The relationship between recombination variation and haplotype polymorphism is shown for the first time in pigs.

A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon Salmo salar populations

Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identified that are easy to use and provide a high level of differentiation power.

Characterization of porcine ASB6 gene and transcripts-comparison of mammalian transcripts

A member of the porcine Ankyrin repeat and suppressor of cytokine signaling (SOCS) Box protein family (ASB), designed as ASB6, was sequenced and the genomic organization of the six exons was determined. We present here a detailed analysis of ASB6 transcripts in pigs. We demonstrate the existence of an alternative transcript resulting from intron retention. This secondary transcript, if functional, encodes a protein without SOCS box. A comparison of mammalian ASB6 transcripts is performed to demonstrate the importance of transcripts encoding for a truncated ASB6 protein.

Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations

A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.

Effects of quantitative trait loci on chromosomes 1, 2, 4, and 7 on growth, carcass, and meat quality traits in backcross Meishan x Large White pigs

The aim of this work was to estimate whether genetic dissection of QTL on chromosomes 1, 2, 4, and 7, detected in an F2 Meishan x Large White population, can be achieved with a recombinant back-cross progeny test approach. For this purpose, a first generation of backcross (BC1) was produced by using frozen semen of F1 Large White x Meishan boars with Large White females. Four BC1 boars were selected because of their heterozygosity for at least 1 of the 4 regions. The BC1 boars were crossed with Large White sows, and the resulting BC2 offspring were measured for several growth and body composition traits. Contrary to the F2 animals, BC2 animals were also measured for meat quality traits in adductor, gluteus superficialis (GS), longissimus dorsi, and biceps femoris (BF) muscles. Each BC1 boar was tested for a total of 39 traits and for the 4 regions with statistical interval mapping analyses. The QTL effects obtained in BC1 families showed some differences compared with those described in F1 families. However, we confirmed QTL effects for growth in the SW1301-SW2512 markers interval on chromosome 1 and also for body composition in the SW1828-SW2512 markers interval on chromosome 1, in the SW2443-SWR783 markers interval on chromosome 2, and in the SW1369-SW632 markers interval on chromosome 7. In addition, we detected new QTL for growth traits on chromosome 2 and for meat quality traits on chromosomes 1 and 2. Growth of animals from weaning to the end of the test was influenced by the IGF2 gene region on chromosome 2. Concerning meat quality, ultimate pH of adductor, longissimus dorsi, and BF were affected by the interval delimited by UMNP3000 and SW2512 markers on chromosome 1, and a* of GS, L* of BF, and water-holding capacity of GS were affected by QTL located between marker loci SW2443 and SWR783 on chromosome 2. Recombinant progeny testing appeared to be a suitable strategy for the genetic dissection of the QTL investigated.