Evidence for three highly significant QTL for meat quality traits in the Finnish Yorkshire pig breed

Evidence for and localization of proposed causative variants in cattle and pig genomes

BACKGROUND

This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding.

RESULTS

For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome.

CONCLUSIONS

Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.

Whole-genome sequencing association analysis reveals the genetic architecture of meat quality traits in Chinese Qingyu pigs

The Chinese Qingyu pig breed is an invaluable indigenous genetic resource. However, few studies have investigated the genetic architecture of meat quality traits in Qingyu pigs. Here, 30 purebred Qingyu pigs were subjected to whole-genome sequencing. After quality control, 18 436 759 SNPs were retained. Genome-wide association studies (GWAS) were then performed for meat pH and color at three postmortem time points (45 min, 24 h, and 48 h) using single-marker regression analysis. In total, 11 and 69 SNPs were associated with meat pH and color of the longissimus thoracis muscle (LTM), respectively, while 54 and 29 SNPs were associated with meat pH and color of the semimembranosus muscle (SM), respectively. Seven SNPs associated with pork pH were shared by all three postmortem time points. Several candidate genes for meat traits were identified, including four genes (CXXC5, RYR3, BNIP3, and MYCT1) related to skeletal muscle development, regulation of Ca²⁺ release in the muscle, and anaerobic respiration, which are promising candidates for selecting superior meat quality traits in Qingyu pigs. To our knowledge, this is the first study investigating the postmortem genetic architecture of pork pH and color in Qingyu pigs. Our findings further the current understanding of the genetic factors influencing meat quality.

Detection of Selection Signatures in Chinese Landrace and Yorkshire Pigs Based on Genotyping-by-Sequencing Data

The domestic pigs have been undergone intense selection pressures for these development of interested traits following domestication and modern breeding. This has altered many traits in most of pig breeds, such as growth rate, body weight, fertility, and immunity. Thus, the objectives of this study were to (1) detect these selection signatures and identify the candidate genes that show evidences of recent artificial selection at the level of whole genome, (2) be beneficial to understand the relationship between genomic structure and phenotypic diversity, and (3) highlight the key roles of these candidate genes in growth and development in the two breeds. The data consisted of total raw number of 345570 single nucleotide polymorphisms (SNPs) in 1200 individuals from the Chinese Landrace pigs (L, n = 600) and Yorkshire pigs (Y, n = 600). Based on these SNPs data, two complementary methods, population differentiation (Fst) and composite likelihood ratio test (CLR), were carried out to detect the selection signatures in this study. A total of 540 potential selection regions (50 kb) which contained 111 candidate genes were detected for Landrace-Yorkshire pair (L-Y) by Fst. In addition, 73 and 125 candidate genes were found for Landrace pigs and Yorkshire pigs by CLR test based on 321 and 628 potential selection regions, respectively. Some candidate genes are associated with important traits and signaling pathways including the ACACA, MECR, COL11A1, GHR, IGF1R, IGF2R, IFNG, and MTOR gene. The ACACA and MECR gene are related to fatty acid biosynthesis. The COL11A1 gene is essential for the development of the normal differentiation. The GHR, IGF1R, and IGF2R gene are significant candidate genes which play major roles in the growth and development in animals. The IFNG gene is associated with some aspects of immune response. The MTOR gene regulates many signaling pathways and signaling transduction pathway.

Deep sequencing of a QTL-rich region spanning 128-136Mbp of pig chromosome 15

The present study shows the characterization of the chromosome 15 (SSC15) region that is highly rich in quantitative traits loci (QTLs) associated with pork quality, growth performance, fat and meat carcass contents. The analytic method that was utilized included targeted enrichment DNA sequencing and RNA hybridisation probes. The research included two pig breeds (Puławska and Polish Landrace) that are significantly different in terms of carcass and meat quality features. Filtered sequences were aligned to the Sscrofa10.2 assembly genome with the STAR aligner and GATK HaplotypeCaller was used for identified gene variants in SSC15 region. In Puławska pigs, which were characterized by high meat quality, mutations were predominantly observed in non-coding regions such as introns and intergenic regions. The highest over 50% frequencies of alternate alleles were identified in the introns of TNS1, VIL1 and USP37 genes. In the upstream gene regions of the Polish Landrace pigs, were observed more mutations than in the upstream gene regions of Puławska. The present study showed interesting gene variant panel that could be analyzed in the further association studies in order to understand the impact on important productive pig traits.

Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits

Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL, protein content (PRO) and CY ( < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO ( < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.

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

Background

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

Results

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

Conclusions

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

Association study between single nucleotide polymorphisms in porcine genes and pork quality traits for fresh consumption and processing into Italian dry-cured ham

Single nucleotide polymorphisms (SNPs) of six genes (TTN, PRKAG3, CAST, CTSB, CTSF, and MYPN), known for associations with carcass and meat quality traits, post mortem proteolysis, were screened in a commercial crossed population of 368 heavy pigs (Large White x Landrace)×Duroc, reared according to the rules of Italian Protected Designation of Origin (PDO) dry-cured ham. Carcass, longissimus thoracis et lumborum muscle (LTL), and green ham traits were obtained after slaughtering, main weight losses of dry-cured hams were collected during processing. The results showed the impact of CAST variants on carcass weight, of CTSF on LTL tenderness, ham weight and fatness, of PRKAG3 and TTN on ultimate pH, hamweight. This study, while confirming significant associations between SNPs of genes and qualitative traits of carcass, longissimus and ham, supports CTSF as candidate gene suitable for fresh consumption purpose (tenderness of longissimus at 24h post mortem), and for dry-cured ham processing (higher thickness of ham subcutaneous fat).

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

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

Implementing meta-analysis from genome-wide association studies for pork quality traits

Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.

Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs

Background

Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare.

Results

Six genomic regions were shown to affect loin pH and Minolta colour a* and b* on both loin and ham through GWAS in 1943 crossbred commercial pigs. Five of them, located on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, SSC16 and SSCX, were associated with meat colour. However, the most promising region was detected on SSC15 spanning 133–134 Mb which explained 3.51% - 17.06% of genetic variance for five measurements of pH and colour. Three SNPs (ASGA0070625, MARC0083357 and MARC0039273) in very strong LD were considered most likely to account for the effects in this region. ASGA0070625 is located in intron 2 of ZNF142, and the other two markers are close to PRKAG3, STK36, TTLL7 and CDK5R2. After fitting MARC0083357 (the closest SNP to PRKAG3) as a fixed factor, six SNPs still remained significant for at least one trait. Four of them are intragenic with ARPC2, TMBIM1, NRAMP1 and VIL1, while the remaining two are close to RUFY4 and CDK5R2. The gene network constructed demonstrated strong connections of these genes with two major hubs of PRKAG3 and UBC in the super-pathways of cell-to-cell signaling and interaction, cellular function and maintenance. All these pathways play important roles in maintaining the integral architecture and functionality of muscle cells facing the dramatic changes that occur after exsanguination, which is in agreement with the GWAS results found in this study.

Conclusions

There may be other markers and/or genes in this region besides PRKAG3 that have an important effect on pH and colour. The potential markers and their interactions with PRKAG3 require further investigation

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users.

MicroRNA expression profiling of lactating mammary gland in divergent phenotype swine breeds

MicroRNA (miRNA) plays a key role in development and specific biological processes, such as cell proliferation, differentiation, and apoptosis. Extensive studies of mammary miRNAs have been performed in different species and tissues. However, little is known about porcine mammary gland miRNAs. In this study, we report the identification and characterization of miRNAs in the lactating mammary gland in two distinct pig breeds, Jinhua and Yorkshire. Many miRNAs were detected as significantly differentially expressed between the two libraries. Among the differentially expressed miRNAs, many are known to be related to mammary gland development and lactation by interacting with putative target genes in previous studies. These findings suggest that miRNA expression patterns may contribute significantly to target mRNA regulation and influence mammary gland development and peak lactation performance. The data we obtained provide useful information about the roles of miRNAs in the biological processes of lactation and the mechanisms of target gene expression and regulation.

A combination of two variants in PRKAG3 is needed for a positive effect on meat quality in pigs

BACKGROUND

Color and pH of meat measured 24 h post mortem are common selection objectives in pig breeding programs. Several amino acid substitutions in PRKAG3 have been associated with various meat quality traits. In our previous study ASGA0070625, a SNP next to PRKAG3, had the most significant association with meat quality traits in the Finnish Yorkshire. However, the known amino acid substitutions, including I199V, did not show any association. The aims of this study were to characterize further variation in PRKAG3 and its promoter region, and to test the association between these variants and the pH and color of pork meat.

RESULTS

The data comprised of 220 Finnish Landrace and 230 Finnish Yorkshire artificial insemination boars with progeny information. We sequenced the coding and promoter region of PRKAG3 in these and in three additional wild boars. Genotypes from our previous genome-wide scans were also included in the data. Association between SNPs or haplotypes and meat quality traits (deregressed estimates of breeding values from Finnish national breeding value estimation for pH, color lightness and redness measured from loin or ham) was tested using a linear regression model. Sequencing revealed several novel amino acid substitutions in PRKAG3, including K24E, I41V, K131R, and P134L. Linkage disequilibrium was strong among the novel variants, SNPs in the promoter region and ASGA0070625, especially for the Yorkshire. The strongest associations were observed between ASGA0070625 and the SNPs in the promoter region and pH measured from loin in the Yorkshire and between I199V and pH measured from ham in the Landrace. In contrast, ASGA0070625 was not significantly associated with meat quality traits in the Landrace and I199V not in the Yorkshire. Haplotype analysis showed a significant association between a haplotype consisting of 199I and 24E alleles (or g.-157C or g.-58A alleles in the promoter region) and pH measured from loin and ham in both breeds (P-values varied from 1.72 × 10⁻⁴ to 1.80 × 10⁻⁸).

CONCLUSIONS

We conclude that haplotype g.-157C - g.-58A - 24E - 199I in PRKAG3 has a positive effect on meat quality in pigs. Our results are readily applicable for marker-assisted selection in pigs.

Genome wide screening of candidate genes for improving piglet birth weight using high and low estimated breeding value populations

Birth weight is an economically important trait in pig production because it directly impacts piglet growth and survival rate. In the present study, we performed a genome wide survey of candidate genes and pathways associated with individual birth weight (IBW) using the Illumina PorcineSNP60 BeadChip on 24 high (HEBV) and 24 low estimated breeding value (LEBV) animals. These animals were selected from a reference population of 522 individuals produced by three sires and six dam lines, which were crossbreds with multiple breeds. After quality-control, 43,257 SNPs (single nucleotide polymorphisms), including 42,243 autosomal SNPs and 1,014 SNPs on chromosome X, were used in the data analysis. A total of 27 differentially selected regions (DSRs), including 1 on Sus scrofa chromosome 1 (SSC1), 1 on SSC4, 2 on SSC5, 4 on SSC6, 2 on SSC7, 5 on SSC8, 3 on SSC9, 1 on SSC14, 3 on SSC18, and 5 on SSCX, were identified to show the genome wide separations between the HEBV and LEBV groups for IBW in piglets. A DSR with the most number of significant SNPs (including 7 top 0.1% and 31 top 5% SNPs) was located on SSC6, while another DSR with the largest genetic differences in F_ST was found on SSC18. These regions harbor known functionally important genes involved in growth and development, such as TNFRSF9 (tumor necrosis factor receptor superfamily member 9), CA6 (carbonic anhydrase VI) and MDFIC (MyoD family inhibitor domain containing). A DSR rich in imprinting genes appeared on SSC9, which included PEG10 (paternally expressed 10), SGCE (sarcoglycan, epsilon), PPP1R9A (protein phosphatase 1, regulatory subunit 9A) and ASB4 (ankyrin repeat and SOCS box containing 4). More importantly, our present study provided evidence to support six quantitative trait loci (QTL) regions for pig birth weight, six QTL regions for average birth weight (ABW) and three QTL regions for litter birth weight (LBW) reported previously by other groups. Furthermore, gene ontology analysis with 183 genes harbored in these 27 DSRs suggested that protein, metal, ion and ATP binding, viral process and innate immune response present important pathways for deciphering their roles in fetal growth or development. Overall, our study provides useful information on candidate genes and pathways for regulating birth weight in piglets, thus improving our understanding of the genetic mechanisms involved in porcine embryonic or fetal development.