Duroc Population Research Articles

8. Genome-wide association study (GWAS) of growth, carcass, and meat quality traits in a French Duroc population under selection

8. Genome-wide association study (GWAS) of growth, carcass, and meat quality traits in a French Duroc population under selection

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs.

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population

BackgroundAlthough the accumulation of whole-genome sequencing (WGS) data has accelerated the identification of mutations underlying complex traits, its impact on the accuracy of genomic predictions is limited. Reliable genotyping data and pre-selected beneficial loci can be used to improve prediction accuracy. Previously, we reported a low-coverage sequencing genotyping method that yielded 11.3 million highly accurate single-nucleotide polymorphisms (SNPs) in pigs. Here, we introduce a method termed selective linkage disequilibrium pruning (SLDP), which refines the set of SNPs that show a large gain during prediction of complex traits using whole-genome SNP data.ResultsWe used the SLDP method to identify and select markers among millions of SNPs based on genome-wide association study (GWAS) prior information. We evaluated the performance of SLDP with respect to three real traits and six simulated traits with varying genetic architectures using two representative models (genomic best linear unbiased prediction and BayesR) on samples from 3579 Duroc boars. SLDP was determined by testing 180 combinations of two core parameters (GWAS P-value thresholds and linkage disequilibrium r2). The parameters for each trait were optimized in the training population by five fold cross-validation and then tested in the validation population. Similar to previous GWAS prior-based methods, the performance of SLDP was mainly affected by the genetic architecture of the traits analyzed. Specifically, SLDP performed better for traits controlled by major quantitative trait loci (QTL) or a small number of quantitative trait nucleotides (QTN). Compared with two commercial SNP chips, genotyping-by-sequencing data, and an unselected whole-genome SNP panel, the SLDP strategy led to significant improvements in prediction accuracy, which ranged from 0.84 to 3.22% for real traits controlled by major or moderate QTL and from 1.23 to 11.47% for simulated traits controlled by a small number of QTN.ConclusionsThe SLDP marker selection method can be incorporated into mainstream prediction models to yield accuracy improvements for traits with a relatively simple genetic architecture, however, it has no significant advantage for traits not controlled by major QTL. The main factors that affect its performance are the genetic architecture of traits and the reliability of GWAS prior information. Our findings can facilitate the application of WGS-based genomic selection.

Factors affecting the accuracy of genomic prediction in joint pig populations.

Genomic prediction (GP) has greatly advanced animal and plant breeding over the past two decades. GP in joint populations is a feasible method to improve the accuracy of genomic estimated breeding values in small populations. However, there is still a need to understand the factors that influence GP in joint populations. This study used simulated data and real data from Duroc pig populations to examine the impact of linkage disequilibrium (LD), causal variants effect sizes (CVESs), and minor allele frequencies (MAF) of SNPs on the accuracy of genomic prediction in joint populations. Three prediction methods were used: genomic best linear unbiased prediction (GBLUP), single-step GBLUP and multi-trait GBLUP. Results from the simulated datasets showed that the accuracies of GP in joint populations were always higher than those in a single population when only LD inconsistencies existed. However, single-step GBLUP accuracy in joint populations decreased as the correlation of MAF between populations decreased, while the accuracy of GBLUP is consistently higher in joint populations than in a single population. As the correlation of CVES between populations decreased, the accuracy of both GBLUP and single-step GBLUP in joint populations declined. Analysis of real Duroc populations showed low genetic correlation, similar to the simulated relationship between the most distant populations. In most cases in Duroc populations, GP have higher accuracies in joint populations than in individual population. In conclusion, the consistency of CVES plays a more important role in multi-population GP. The genetic relatedness of the Duroc populations is so weak that the prediction accuracy of GP in joint populations is reduced in some traits. Multi-trait GBLUP is a competitive method for the joint breeding evaluation.

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs.

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines.

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

Exploiting single-marker and haplotype-based genome-wide association studies to identify QTL for the number of teats in Italian Duroc pigs

The number of teats is a morphological trait of high economic relevance for the pig industry. Here, to dissect the genomic architecture of this trait in the Italian Duroc pig population, we present the results of genome-wide association studies in this Italian heavy pig breed. A total of 1,162 pigs, for which the number of teats was recorded, was genotyped with two high-throughput single nucleotide polymorphism (SNP) genotyping platforms (60 K and 70 K). Genome-wide association analyses were based on a single-marker approach and on a haplotype-based approach. Two quantitative trait loci (QTL) affecting the number of teats were identified. The most significant QTL, identified by the single-marker analysis and confirmed by the haplotype-based method, was located on Sus scrofa chromosome (SSC) 7, in the region of the vertnin (VRTN) gene. Suggestively associated markers (SNPs and haplotypes) were located on SSC10, in the region of the FERM domain containing 4A (FRMD4A) gene, the second identified QTL. These findings confirm previous results obtained in a few other Duroc populations. Overall, this study further supported the important role of variability in the VRTN gene region in affecting the number of teats in pigs. Moreover, the results also indicated that this trait in the Italian Duroc breed, as in many other pig breeds, is affected by few QTL, with the contribution of many other genetic factors with small effects, following the classical theory of quantitative traits.

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis.

Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1, and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1, and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggest that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Polymorphisms of Candidate Genes Associated with Growth and Carcass Traits in Canadian Duroc Pigs

Background: Selection based on traits such as average daily gain (ADG) and carcass quality in commercial pig populations have drawn attention of swine breeders due to the correlation with growth and consumer preference for carcass composition, respectively. The association between melanocortin 4 receptor (MC4R) gene, which encodes the G-protein-coupled receptor and ADG and carcass quality, have been well documented. The study was conducted to determine the effects of MC4R/TaqI and PIT-1/RsaI polymorphisms on growth and carcass quality traits in total of 576 Duroc pigs at national breeding farms of Vietnam. Methods: After the performance test, the desired traits including ADG, IF and LD were measured. ADG (g/day) was calculated as the live weight divided by the number of days from birth to 100 kg, BF and LD can be captured at position P2 (6-8 cm away from body midline at the last rib level) with Ultrasound machine Aloska SSD 500V. Genomic DNA were collected and genotyped to observe the polymorphism of MC4R and PIT-1. Result: Three genotypes AA, AG andGG of MC4R gene and AA, AB and BB of PIT-1 gene were found in the studied pig population. The observed frequencies of AA, AG and GG were 0.09, 0.41 and 0.50 (MC4R gene) and for AA, AB and BB were 0.37, 0.47 and 0.16, respectively. The G allele (MC4R) and B allele (PIT-1) have more positive effects on traits of ADG, BF and LD. Specifically, in MC4R gene, the individuals carrying GG genotype had higher ADG by 50 gram and lower BF by 1.4 mm than AA genotype. In PIT-1 gene, pigs carrying BB genotype had higher ADG and LD than AA genotype by 37 gram and by 1.9 mm, respectively. Therefore, the increased selection of G allele, GG genotype (MC4R) and of B allele, BB genotype (PIT-1) should be considered to contribute to the improvement of ADG, BF and LD traits in Duroc population in current study

Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs

With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.

A natural knockout of the MYO7A gene leads to pre-weaning mortality in pigs.

SummaryThe pig breeding system provides a unique framework to study recessive defects and the consequence on the phenotype. We examined a commercial synthetic Duroc population for recessive defects and identified a haplotype on chromosome 9 significantly affecting pre‐weaning mortality. To identify the causal variant underlying the mortality, we examined sequence data of four carrier animals and 21 non‐carrier animals from the same population. The results yield a strong candidate causal stop‐gained variant (NM_001099928.1:c.541C>T) affecting the MYO7A gene in complete linkage disequilibrium with the lethal haplotype. The variant leads to an impaired (p.Gln181*) MYO7A protein that truncates 2032 amino acids from the protein. We examined a litter from a carrier sow inseminated by a carrier boar. From the resulting piglets, two confirmed homozygous piglets suffered from severe balance difficulties and the inability to walk properly. The variant segregates at a carrier frequency of 8.2% in the evaluated population and will be gradually purged from the population, improving animal welfare. Finally, this 'natural knockout' will increase our understanding of the functioning of the MYO7A gene and provides a potential model for Usher syndrome in humans.

Exploring the genetic features and signatures of selection in South China indigenous pigs

To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism (SNP) BeadChips. Principal component analysis (PCA), effective population size (Ne), linkage disequilibrium (LD), and signatures of selection were explored and investigated among the six pig populations. The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago. The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population. However, the LD of all six pig populations showed the opposite order at long distances (>5 Mb). Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs. Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.

Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality.

With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc’s excellent phenotypic traits.

Genetic structure and population dynamics of autochthonous and modern porcine breeds. Analysis of the IGF2 and MC4R genes that determine carcass characteristics

To know the genetic situation of the Pampa Rocha, Celta, Bizaro Portuguese, Duroc, Iberian Extremeno and Iberian Andalusian porcine populations, their genetic structure and population dynamics were studied on the IGF2 and MC4R genes, which determine meat characteristics and quality. The degree of genetic variability (He = 0.2511 in Pampa Rocha; 0.0278 in Celta; 0,1453 in Bizaro Portuguese; 0.3719 in Duroc; 0.0764 in Iberian Extremeno and 0.0384 in Iberian Andalusian), genetic distance, and the presence or absence of consanguinity were studied. The Fis values were positive for the Duroc population (0.00426) indicating a very low inbreeding, the rest of the populations did not present consanguinity. Significant deviations (P ≤ 0.05) in the Hardy-Weinberg (HW) equilibrium were obtained for the IGF2 locus in Celta, Iberian Extremeno, and Iberian Andalusian populations with the G allele fixed, while the Bizaro Portuguese, Pampa Rocha, and Duroc populations presented polymorphism, the G allelic frequency was much higher than A allele, except in the Duroc breed (0.15). These findings could help breeders to increase the presence of the A allele for the improvement of muscle mass and reduction in the back-fat thickness in this breed. All the studied populations presented polymorphism for the MC4R locus with different frequencies for each allele. Furthermore, these results could allow developing strategies against anthropogenic activities that hinder the conservation of the biodiversity of these porcine breeds.

The SSC15 QTL-Rich Region Mutations Affecting Intramuscular Fat and Production Traits in Pigs

Abstract One of the more interesting regions in the pig genome is on chromosome 15 (115,800,000-122,100,000, SSC15, Sus scrofa 11.1) that has high quantitative trait locus (QTL) density associated with fattening, slaughter and meat quality characteristics. The SSC15 region encodes over 80 genes and a few miRNA sequences where potential genetic markers can be found. The goal of the study was to evaluate the effects of SSC15 mutations associated with villin 1 (VIL1), tensin 1 (TNS1), obscurin-like 1 (OBSL1) genes and with one long non-coding RNA (lncRNA) on productive pig traits and to enrich the genetic marker pool in further selection purpose. The potential genetic markers were identified using the targeted enrichment DNA sequencing (TEDNA-seq) of chromosome 15 region. The selected mutations were genotyped by using HRM, PCR and PCRRFLP methods. The association study was performed using the general linear model (GLM) in the sas program that included over 600 pigs of 5 Polish populations. The rs332253419 VIL1 mutation shows a significant effect on intramuscular fat (IMF) content in Duroc population where AA pigs had a 16% higher level than heterozygotes. The IMF content is also affected by the OBSL1 mutation, and the differences between groups are even up to 30%, but it is strongly dependent on breed factor. The OBSL1 mutation also significantly influences the meat yellowness, backfat thickness and pH level. The performed study delivers valuable information that could be highly useful during the development of the high-throughput genotyping method for further selection purposes in pigs. The OBSL1 and VIL1 mutations seem to be the most promising DNA marker showing a high effect on IMF level.

Genetic parameters of sow feed efficiency during lactation and its underlying traits in a Duroc population

As a result of the genetic selection for prolificacy and the improvements in the environment and farms management, litter size has increased in the last few years so that energy requirements of the lactating sow are greater. In addition, selection for feed efficiency of growing pigs is also conducted in maternal lines, and this has led to a decrease in appetite and feed intake that is extended to the lactation period, so the females are not able to obtain the necessary energy and nutrients for milk production and they mobilize their energetic reserves. When this mobilization is excessive, reproductive and health problems occur which ends up in an early sow culling. In this context, it has been suggested to improve feed efficiency at lactation through genetic selection. The aim of this study is to know, in a Duroc population, the genetic determinism of sow feed efficiency during lactation and traits involved in its definition, as well as genetic and environmental associations between them. The studied traits are daily lactation feed intake (dLFI), daily sow weight balance (dSWB), backfat thickness balance (BFTB), daily litter weight gain (dLWG), sow residual feed intake (RFI) and sow restricted residual feed intake (RRFI) during lactation. Data corresponded to 851 parities from 581 Duroc sows. A Bayesian analysis was performed using Gibbs sampling. A four-trait repeatability animal model was implemented including the systematic factors of batch and parity order, the standardized covariates of sow weight (SWf) and litter weight (LWs) at farrowing for all traits and lactation length for BFTB. The posterior mean (posterior SD) of heritabilities were: 0.09 (0.03) for dLFI, 0.37 (0.07) for dSWB, 0.09 (0.03) for BFTB, 0.22 (0.05) for dLWG, 0.04 (0.02) for RFI and null for RRFI. The genetic correlation between dLFI and dSWB was high and positive (0.74 (0.11)) and null between dLFI and BFTB. Genetic correlation was favourable between RFI and dLFI and BFTB (0.71 (0.16) and −0.69 (0.18)), respectively. The other genetic correlations were not statistically different from zero. The phenotypic correlations were low and positive between dLFI and dSWB (0.27 (0.03), dSWB and BFTB (0.25 (0.04)), and between dLFI and dLWG (0.16 (0.03)). Therefore, in the population under study, the improvement of the lactation feed efficiency would be possible either using RFI, which would not have unfavourable correlated effects, or through an index including its component traits.

Analysis of porcine OSBPL5 gene allelic expression in skeletal muscle and association of a single-nucleotide polymorphism in the coding region with production traits

Genes that exhibit allelic expression imbalance and imprinted genes play important roles in the survival of the embryo and postnatal growth regulation. In this study, the porcine oxysterol-binding protein-related 5 (OSBPL5) gene was examined, and the 2140G>A mutation (rs318687202) was found in its coding region by a comparison of Laiwu and Landrace pigs. By allele-specific expression analysis based on a specific single-nucleotide polymorphism (SNP), the imprinting status of OSBPL5 gene in skeletal muscle from both neonate and adult pigs was determined. The results showed that the OSBPL5 was paternally imprinted in skeletal muscle from adults but biallelically expressed with predominantly maternal imprinting in neonates. The distribution of the 2140G>A SNP in four pig populations was analyzed, which showed that GG genotype was dominant in Duroc and Dapulian populations, whereas the AG genotype was dominant in Junmu-1 and Laiwu populations. Pigs with the GG genotype had significantly larger litters and greater cannon bone circumferences but a lower average daily gain than pigs with the AA genotype. In conclusion, we determined the difference in the allelic expression of OSBPL5 between adult and neonate pigs and identified an SNP in its coding region that is associated with production traits.

About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

BackgroundThe comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTLs with copy number variant regions (CNVR) segregating in this Duroc population.ResultsThe analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis-eQTLs were shared by both tissues (i.e. 42.8% of the cis-eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis-eQTL signals.ConclusionDespite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTLs regulating gene expression in both tissues. Several of these cis-eQTLs influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.

Estimation of genetic parameters and accuracy of genomic prediction for production traits in Duroc pigs

Abstract: Genetic parameters and accuracy of genomic prediction for production traits in a Duroc population were estimated. Data were on 24 828 purebred Duroc pigs born in 2000–2016. After quality control procedures, 30 263 single nucleotide polymorphism markers and 560 animals remained that were used to predict the genomic breeding values of individuals. Accuracies of predicted breeding values for average daily gain (ADG), backfat thickness (BF), loin muscle area (LMA), lean percentage (LP) and age at 90 kg (D90) between pedigree-based and single-step methods were compared. Analyses were carried out with a multivariate animal model to estimate genetic parameters for production traits while univariate analyses were performed to predict the genomic breeding values of individuals. Heritability estimates from pedigree analysis were moderate to high. Heritability estimates and standard error for ADG, BF, LMA, LP and D90 were 0.35 ± 0.01, 0.35 ± 0.11, 0.24 ± 0.04, 0.42 ± 0.11 and 0.37 ± 0.03, respectively. Genetic correlations of ADG with BF and LP were low and negative. Genetic correlations of LMA with ADG, BF, LP and D90 were –0.37, –0.27, 0.48 and 0.31, respectively. High correlations were observed between ADG and D90 (–0.98), and also between BF and LP (–0.93). Accuracies of genomic breeding values for ADG, BF, LMA, LP and D90 were 0.30, 0.33, 0.38, 0.40 and 0.28, respectively. Corresponding accuracies using pedigree-based method were 0.29, 0.32, 0.38, 0.39 and 0.27, respectively. The results showed that the single-step method did not show significant advantage compared to the pedigree-based method.

Pig identification and meat traceability by multiallelic amplification fragments with multiple single nucleotide polymorphisms

Compared with conventional identification methods, DNA-based genetic approaches such as single nucleotide polymorphisms (SNPs) and satellites are much more reliable for pig identification and meat traceability. In this study, multiallelic amplification fragments with multiple SNPs, incorporating the advantages of both SNPs and microsatellites, were explored for the first time for pig identification and meat traceability. Primer pairs for multiallelic fragments and their optimal SNPs were successfully selected and used for identification of individuals from Suzhong and Duroc populations. Meanwhile, the combined panel of the above mentioned primer pairs together with their optimal SNPs for Suzhong and/or Duroc pigs were validated for identification of the hybrids (Suzhong×Duroc). Therefore, we have successfully selected multiallelic amplification fragments with multiple SNPs to identify pigs and their meat samples from Suzhong, Duroc or their hybrids. Our study demonstrates that our method is more powerful for pig identification or meat traceability than SNPs or microsatellites.