Candidate Genes For Meat Quality Research Articles

Identification of SNPs Associated with Goose Meat Quality Traits Using a Genome-Wide Association Study Approach.

(1) Background: Goose meat is highly valued for its economic significance and vast market potential due to its desirable qualities, including a rich nutritional profile, tender texture, relatively low-fat content, and high levels of beneficial unsaturated fatty acids. However, there is an urgent need to improve goose breeding by identifying molecular markers associated with meat quality. (2) Methods: We evaluated meat quality traits, such as meat color, shear force (SF), cooking loss rate (CLR), and crude fat content (CFC), in a population of 215 male Sichuan white geese at 70 days of age. A GWAS was performed to identify potential molecular markers associated with goose meat quality. Furthermore, the selected SNPs linked to meat quality traits were genotyped using the MALDI-TOP MS method. (3) Results: A dataset of 2601.19 Gb of WGS data was obtained from 215 individuals, with an average sequencing depth of 10.89×. The GWAS revealed the identification of 43 potentially significant SNP markers associated with meat quality traits in the Sichuan white goose population. Additionally, 28 genes were identified as important candidate genes for meat quality. The gene enrichment analysis indicated a substantial enrichment of genes within a 1Mb vicinity of SNPs in both the protein digestion and absorption pathway and the Glycerolipid metabolism pathway. (4) Conclusion: This study provides valuable insights into the genetic and molecular mechanisms underlying goose meat quality traits, offering crucial references for molecular breeding in this field.

Genetic Association and Expression of JHDM1A Gene Related to Meat pH in Commercial Pigs

An experiment was conducted to study the association and expression of JHDM1A gene as a candidate gene for meat quality. The polymorphism was genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using restriction enzyme on a total of 300 muscle samples of [Duroc × (Large White × Landrace)] pigs. Results showed that JHDM1A gene was significantly associated with meat pH 45 min post-mortem (p.m.) (p<0.05). Allele frequencies for G and C were 0.53 and 0.47. The genotype frequencies for GG, GC, and CC were 0.24, 0.58, and 0.18, respectively. The Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) study were analyzed between low and high pH 45 min p.m. groups (n=10 per group) according to the association result. JHDM1A expression was higher in animals with a low post-mortem meat pH 45 min (p<0.05). Therefore, polymorphism and expression in the porcine JHDM1A gene might be the important candidate genes to improve meat quality traits in terms of meat pH.

Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population.

Meat quality is an important trait for pig-breeding programs aiming to meet consumers’ demands. Geneticists must improve meat quality based on their understanding of the underlying genetic mechanisms. Previous studies showed that most meat-quality indicators were low-to-moderate heritability traits; therefore, improving meat quality using conventional techniques remains a challenge. Here, we performed a genome-wide association study of meat-quality traits using the GeneSeek Porcine SNP50K BeadChip in 582 crossbred Duroc × (Landrace × Yorkshire) commercial pigs (249 males and 333 females). Meat conductivity, marbling score, moisture, meat color, pH, and intramuscular fat (IMF) content were investigated. The genome-wide association study was performed using both fixed and random model Circulating Probability Unification (FarmCPU) and a mixed linear model (MLM) with the rMVP software. The genomic heritability of the studied traits ranged from 0.13 ± 0.07 to 0.55 ± 0.08 for conductivity and meat color, respectively. Thirty-two single-nucleotide polymorphisms (SNPs) were identified for meat quality in the crossbred pigs using both FarmCPU and MLM. Among the detected SNPs, five, nine, seven, four, six, and five were significantly associated with conductivity, IMF, marbling score, meat color, moisture, and pH, respectively. Several candidate genes for meat quality were identified in the detected genomic regions. These findings will contribute to the ongoing improvement of meat quality, meeting consumer demands and improving the economic outlook for the swine industry.

Sequence and haplotypes of ankyrin 1 gene (ANK1) and their association with carcass and meat quality traits in yak.

Ankyrin 1 (ANK1) gene has been demonstrated to be a functional candidate gene for meat quality that helps to constitute and maintain the structure of the cell skeleton. In this study, three contiguous ANK1 regions from yak were analyzed using polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP). As a result, nine single-nucleotide polymorphisms (SNPs) were identified, four of them in the coding region and three (c.179 C/A, c.250 G/C, and c.313 C/T) putatively resulting in amino acid changes (p. Ala 60 Glu, p. Asp 84 His, and p. Pro 105 Ser). Some SNPs in promoter region were located within or nearby the putative transcription factor binding sites, such as Sp1 and GATA, which might have an impact on the expression of the yak ANK1 gene. The presence of C1-D3 and C1-A3 were associated with an increased hot carcass weight (p = 0.0045) and a decreased drip loss rate (p = 0.0046). The presence of B1-B3, C1-A3 and C1-D3 had decreased Warner-Bratzler shear force (p = 0.0066, p = 0.0343 and p = 0.0004). The presence of one and two copies of B1-B3 and C1-A3 had decreased Warner-Bratzler shear force (p = 0.0005 and p = 0.0443), and C1-A3 had also decreased drip loss rate (p = 0.0164). These findings indicated that genetic variations of the ANK1 gene would be a preferable biomarker for the improvement of yak meat quality.

Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

BackgroundGenetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits.ResultsUsing a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3).ConclusionsThe present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.

Evolution of peroxisomal trans-2-enoyl-CoA reductase (PECR) as candidate gene for meat quality

Peroxisomal trans-2-enoyl-CoA reductase plays a role in fatty acid elongation via the conversion of 2E-Octadecenoyl-coA to stearoyl-coA. It is encoded by the PECR gene, which is located in a QTL-rich region on chromosome 15 in pigs. Due to the function and localization of this gene, it could be supposed that it contains potential biomarkers. Therefore, in the present study regulatory sequences of the PECR gene has been analyzed. DNA was isolated from blood samples of three pig breeds: Polish Landrace (n=359), Polish Large White (n=316) and Puławska pigs (n=140). The identification of PECR mutations was performed by High-Resolution Melting and Sanger sequencing methods, and genotyping by PCR-RFLP. The association study was performed using the GLM SAS procedure. In the second part of the experiment, the profile of PECR expression dependent on pig breed and PECR genotype was evaluated (n=10 in each analyzed group) by using qPCR method and Taqman probes. A single nucleotide substitution ENSSSCT00000030284.1: c.−145T>C in a promoter region of PECR gene was found which probably alters the binding site for transcription factors. The association study showed that PECR polymorphism affects the main carcass cuts, IMF and meat texture parameters. Pigs with a TT genotype were characterized by ↓weight of ham, ↑weight of loin, ↓IMF, ↑backfat thickness, ↓loin and ↑ham texture parameters (P<0.05). The results obtained also showed that the PECR transcript profile is dependent on pig breed (P<0.001) and c.−145T>C PECR genotype (P<0.05). The T allele in Polish pig populations is rather rare. However, information concerning the effect of PECR mutation on pig traits may have significant impact in populations where the T allele is more frequent and during development of a method of genomic estimated breeding values (GEBV) in pigs.

Genomic structure, expression and association study of the porcine FSD2

The fibronectin type III and SPRY domain containing 2 (FSD2) on porcine chromosome 7 is considered a candidate gene for pork quality, since its two domains, which were present in fibronectin and ryanodine receptor. The fibronectin type III and SPRY domains were first identified in fibronectin and ryanodine receptor, respectively, which are candidate genes for meat quality. The aim of this study was to elucidate the genomic structure of FSD2 and functions of single nucleotide polymorphisms (SNPs) within FSD2 that are related to meat quality in pigs. Using a bacterial artificial chromosome clone sequence, we revealed that porcine FSD2 consisted of 13 exons encoding 750 amino acids. In addition, FSD2 was expressed in heart, longissimus dorsi muscle, psoas muscle, and tendon among 23 kinds of porcine tissues tested. A total of ten SNPs, including four missense mutations, were identified in the exonic region of FSD2, and two major haplotypes were obtained based on the SNP genotypes of 633 Berkshire pigs. Both haplotypes were associated significantly with intramuscular fat content (IMF, P<0.020) and moisture percentage (MP, P<0.002). Moreover, haplotype 2 was associated with meat color, affecting yellowness (P=0.002). These haplotype effects were further supported by the alteration of putative protein structures with amino acid substitutions. Taken together, our results suggest that FSD2 haplotypes are involved in regulating meat quality including IMF, MP, and meat color in pigs, and may be used as meaningful molecular makers to identify pigs with preferable pork quality.

Polymorphisms in the regulatory region of the porcine MYLPF gene are related to meat quality traits in the Large White breed

The MYLPF gene encodes fast myosin regulatory light chain, and is a positional and functional candidate gene for meat quality. The aim of this study was to identify associations between SNPs in the promoter region of the porcine MYLPF gene and meat quality traits. A total of 22 SNPs were identified in a population of crossbred animals (n=86) and based on minor allele frequency and proximity to the transcription start site, five SNPs were genotyped in purebred; Large White (n=98), Duroc (n=99) and Pietrain (n=98) pigs. No associations were observed in the Pietrain breed, while the Duroc breed was almost monomorphic for all SNPs. In the Large White breed SNP g-1314A>G and linked SNPS g.-871T>G, g.-566T>C, g.-403C>G were associated with ultimate pH and driploss (P<0.05). This study identified associations between MYLPF and meat quality and highlights the importance of considering the genetic background within gene-assisted selection programmes.

Molecular cloning, sequence analysis and tissue-specific expression of Akirin2 gene in Tianfu goat

The Akirin2 gene is a nuclear factor and is considered as a potential functional candidate gene for meat quality. To better understand the structures and functions of Akirin2 gene, the cDNA of the Tianfu goat Akirin2 gene was cloned. Sequence analysis showed that the Tianfu goat Akirin2 cDNA full coding sequence (CDS) contains 579bp nucleotides that encode 192 amino acids. A phylogenic tree of the Akirin2 protein sequence from the Tianfu goat and other species revealed that the Tianfu goat Akirin2 was closely related with cattle and sheep Akirin2. RT-qPCR analysis showed that Akirin2 was expressed in the myocardium, liver, spleen, lung, kidney, leg muscle, abdominal muscle and the longissimus dorsi muscle. Especially, high expression levels of Akirin2 were detected in the spleen, lung, and kidney whereas lower expression levels were seen in the liver, myocardium, leg muscle, abdominal muscle and longissimus dorsi muscle. Temporal mRNA expression showed that Akirin2 expression levels in the longissimus dorsi muscle, first increased then decreased from day 1 to month 12. Western blotting results showed that the Akirin2 protein was only detected in the lung and three skeletal muscle tissues.

New Polymorphisms in Regulatory Region of CAPN3 Gene with no Effect on Gene Expression in Breast Muscle of Broiler Chickens

Abstract Calpains are enzymes that belong to calcium-dependent, non-lysosomal cysteine proteases. The CAPN3 gene encodes a major intracellular specific muscle protease with a high capacity for degradation of cytoskeletal and muscle fibre proteins. Therefore, they play an important role in fusion of myoblasts, proliferation, cell growth and migration. In chickens, the gene encoding for calpain 3 is localized on chromosome 5. Due to the function of encoded protein, the CAPN3 has beenchosen as a candidate gene for meat quality in chickens. Consequently, the aim of our study was to identify new polymorphisms in the regulatory region of CAPN3 gene and to investigate their impact on CAPN3 transcript abundance in breast muscles. The experiment used broilers of two genetic lines: fast- and slow-growing. The polymorphisms were identified by screening with High Resolution Melting (HRM) and sequencing based on the Sanger method. The CAPN3 gene expression was conducted by using succinate dehydrogenase complex, subunit A (SDHA) and 60S ribosomal protein L4 (RPL4) genes as endogenous controls. Four new polymorphisms were found: g.322176G&gt;A in promoter region (GenBank: AADN03004661.1), c.176*C&gt;T, c.144*G&gt;C and c.137*_147*delCAGCCCTGCTT in 3`UTR sequence. The new polymorphisms were identified by using restriction enzymes ScrFI, BslI, AcuI, HpyAV, respectively. The frequency of polymorphisms found in 3`UTR region was similar in both lines. According to polymorphisms identified in 3`UTR region the alleles with deletion, C and C (c.137*_147*del, c.144*G&gt;C and c.176*C&gt;T) were rare. The polymorphism identified in the promoter region and 3`UTR regions changed a few binding sites for transcription factors, but did not alter any binding sites for the other important translation regulators such as miRNA. Analysis of the effect of new polymorphisms on CAPN3 gene expression showed that in fast-growing line the chickens with GG genotype according to polymorphism g.322176G&gt;A inthe promoter region, were characterized by the highest CAPN3 transcript abundance. Other polymorphisms in 3&gt;UTR region seem to have no effect on CAPN3 gene expression.

Associations between single nucleotide polymorphisms in 33 candidate genes and meat quality traits in commercial pigs

This study aimed to evaluate the effects of single nucleotide polymorphisms (SNPs) in candidate genes for meat quality using a custom 96-SNP panel (Illumina Vera Code GoldenGate Assay) on 15 traits collected from 400 commercial pigs. Meat quality measurements included muscle pH, color (L*, a* and b*), drip loss, cooking loss, peak shear force and six sensory traits including appearance (outside and inside), tenderness, juiciness, flavor and overall liking as well as carcass weight and probe yield. Thirty-five SNPs with minor allele frequencies > 0.10 remained for the multimarker association using the GLM procedure of sas 9.2. Results showed that 20 SNPs were significantly associated with at least one of the traits with either additive or dominance or both effects (P < 0.05). Among these significant SNPs, five of them in ADIPOQ, FTO, TNF, LEPR and AMPD1 had an effect on more than three traits simultaneously; those in MC4R, CAST, DGAT1 and MYF6 had an effect on two traits, while the others were associated with one trait. The results suggest that these markers could be incorporated into commercial pigs for marker-assisted selection and breeding programs for carcass and meat quality trait improvement.

SNP identification in swine candidate genes for meat quality

An important aim of Italian pig selection is to obtain animals having high aptitude for protected designation of origin (PDO) dry-cured ham production. The efforts of the last years were directed to single nucleotide polymorphisms (SNPs) identification for large-scale association studies. In this work, SNPs in seven candidate genes for meat quality traits (inositol polyphosphate-1-phosphatase, INPP1, phosphatidylinositol 3-kinases, PIK3R2, protein tyrosine phosphatase receptor type D, PTPRD, phospholipase C gamma 1, PLCG1, CASP2 and RIPK1 domain containing adaptor with death domain, CRADD, cyclin-dependent kinase inhibitor 1C, CDKN1C, calpain, small subunit 1, CAPNS1) were found analyzing 22 animals representing the extreme tails of the distribution for phenotypes related to meat quality of 231 Large White×Landrace individuals. Association analysis revealed that the CRADD c.343A>G SNP was significant associated with muscle compactness, and the PTPRD c.2449C>A polymorphism and the PIK3R2 c.2966C>T SNP with muscle compactness and backfat thickness. The five SNPs were then analyzed in 560 Italian Large White with extreme EBVs for fat thickness and in 600 individuals belonging to three Italian breeds (Large White, Duroc, Landrace), with extreme estimated breeding values (EBVs) for fat or growth traits. The PIK3R2 c.2966C>T mutation showed significant associations with backfat thickness, average daily gain, feed conversion rate and lean cut yield. The PTPRD c.2680C>T SNP showed a significant association with thigh weight in Large White individuals.

Conservation of Endangered Spanish Cattle Breeds Using Markers of Candidate Genes for Meat Quality

The aim was to analyze the allelic and genotypic frequencies for two genes associated with tenderness of meat (CAPN1 and CAST) and one with fat deposits (DGAT1) in three endangered Spanish cattle breeds: Berrenda en Colorado (BC), Berrenda en Negro (BN), and Cardena Andaluza (CA) to utility of their involvement in the selection of them and to help the adoption of conservation measurement. Seventy-five males and 298 females of those breeds were genotyped. Genotypic and allelic frequencies for each polymorphic locus were estimated. There were significant differences in the genotypic frequencies among breeds in CAPN1 and DGTA1 genes and in the case of the genic frequencies in CAPN1, CAST, and DGAT1 genes. The three breeds analyzed (BC, BN, and CA) presented high allelic frequencies for the favorable allele of the three markers (from 0.41 to 0.75). The association between the favorable allele and meat quality must be confirmed. In cases of association with differences in quality meat, the absence of differences in the genotypic and genic frequency distributions between the sexes is advantageous in mating planning because it implies that there is no handicap to be overcome for the conservation program and it would allow the use of sires to promote the increase in improvements within a short period of time.

Effect of Single Nucleotide Polymorphism of Endothelial Differentiation G-Protein Coupled Receptor 1 (EDG1) Gene on Marbling Score in Hanwoo

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

Polymorphism in coding region of pig &lt;I&gt;PRDX6&lt;/I&gt; gene and its genetic effects analysis

PRDX6, a member of antioxidant protein superfamily, plays an important role in oxidative stress, catabolism of lipids and phospholipid lipisomes. Therefore, we used PRDX6 as an important candidate gene for meat quality according to its physiological and biochemical function. Partial coding sequence of porcine PRDX6 was isolated and two potenial SNPs, one at 417 bp (C/T) and the other at 423 bp (A/G), were found in the fourth exon by comparison of the obtained sequence from different pig breeds. In order to explore the relationship between PRDX6 polymorphism and meat quality, genetic variation and trait association of these two SNPs were separately performed in 6 purebred pig population and 247 F2 "Large White x Meishan" resource population by pyrosequencing. The results showed that allele C was predominant in western pig breeds, while allele T was predominant in Chinese indigenous breeds at 417 bp (C/T). This SNP was significantly associated with the intramuscular fat and water moisture (P < 0.05). The A/G mutation at 423 bp was significantly associated with drip water rate, water holding capacity, intramuscular fat, and water moisture (P < 0.05). Allele A was predominant in western pig breeds, while allele G was predominant in Chinese indigenous breeds. These two SNPs were likely to be important markers affecting meat quality traits (especially the muscle tenderness).

Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

BackgroundRecent QTL and gene expression studies have highlighted ankyrins as positional and functional candidate genes for meat quality. Our objective was to characterise the promoter region of the bovine ankyrin 1 gene and to test polymorphisms for association with sensory and technological meat quality measures.ResultsSeven novel promoter SNPs were identified in a 1.11 kb region of the ankyrin 1 promoter in Angus, Charolais and Limousin bulls (n = 15 per breed) as well as 141 crossbred beef animals for which meat quality data was available. Eighteen haplotypes were inferred with significant breed variation in haplotype frequencies. The five most frequent SNPs and the four most frequent haplotypes were subsequently tested for association with sensory and technological measures of meat quality in the crossbred population. SNP1, SNP3 and SNP4 (which were subsequently designated regulatory SNPs) and SNP5 were associated with traits that contribute to sensorial and technological measurements of tenderness and texture; Haplotype 1 and haplotype 4 were oppositely correlated with traits contributing to tenderness (P < 0.05). While no single SNP was associated with intramuscular fat (IMF), a clear association with increased IMF and juiciness was observed for haplotype 2.ConclusionThe conclusion from this study is that alleles defining haplotypes 2 and 4 could usefully contribute to marker SNP panels used to select individuals with improved IMF/juiciness or tenderness in a genome-assisted selection framework.

Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2

Principal component analysis of traits related to carcass and meat properties were combined with microarray expression data for the identification of functional networks of genes and biological processes taking place during the conversion of muscle to meat. Principal components (PCs) with high loadings of meat quality traits were derived from phenotypic data of 572 animals of a porcine crossbreed population. Microarray data of 74 M. longissimus dorsi samples were correlated with PC datasets. Lists of significantly correlated genes were analyzed for enrichment of functional annotation groups as defined in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases as well as the Ingenuity Pathways Analysis library. Ubiquitination, phosphorylation, mitochondrion dysfunction, actin, integrin, platelet-derived growth factor, epidermal growth factor, vascular endothelial growth factor, and Ca signaling pathways are correlated with meat quality. Among the significantly trait-associated genes, CAPZB, ANKRD1, and CTBP2 are promoted as candidate genes for meat quality that provide a link between the highlighted pathways. Knowledge of the relevant biological processes and the differential expression of members of the pathway will provide tools that are predictive for traits related to meat quality and that may also be diagnostic for many muscle defects or damages including muscle atrophy, dystrophy, and hypoxia.

Polymorphisms in swine candidate genes for meat quality detected by PCR-SSCP

In order to identify SNPs in seven candidate genes for meat quality, PCR-SSCP experiments were carried out. Statistical analyses in a population of 240 individuals identified the animals constituting the extreme tails of the Gaussian distribution for three selected phenotypes: muscle compactness, fat thickness, and the principal component 1. Twenty-two of these animals were chosen for the molecular analyses. Several fragments in the candidate genes were tested by PCR-SSCP and many different patterns were found, indicating the presence of polymorphisms. The polymorphic fragments were sequenced and analyzed. CRADD was the most interesting gene, because many PCR-SSCP patterns were found in the samples. The results will be tested in another Italian Large White population to verify the segregation and the association of SNPs with phenotypes that influence meat quality.

Two new splice variants in porcine PPARGC1A

BackgroundPeroxisome proliferator-activated receptor γ coactivator 1α (PPARGC1A) is a coactivator with a vital and central role in fat and energy metabolism. It is considered to be a candidate gene for meat quality in pigs and is involved in the development of obesity and diabetes in humans. How its many functions are regulated, is however still largely unclear. Therefore a transcription profile of PPARGC1A in 32 tissues and 4 embryonic developmental stages in the pig was constructed by screening its cDNA for possible splice variants with exon-spanning primers.FindingsThis led to the discovery of 2 new splice variants in the pig, which were subsequently also detected in human tissues. In these variants, exon 8 was either completely or partly (the last 66 bp were conserved) spliced out, potentially coding for a much shorter protein of respectively 337 and 359 amino acids (aa), of which the first 291 aa would be the same compared to the complete protein (796 aa).ConclusionConsidering the functional domains of the PPARGC1A protein, it is very likely these splice variants considerably affect the function of the protein and alternative splicing could be one of the mechanisms by which the diverse functions of PPARGC1A are regulated.

Pig KALRN, MYH1, MLC2V, SNX13, AK1, and PPIA loci RH mapping and chromosome position refining

The suppressive subtractive hybridization technique was previously used by the authors to identify candidate genes for meat quality in pig. A set of ESTs homologous (>95%) to genes involved in muscle metabolism is reported in the present paper. Four ESTs homologous to MYH1, KALRN, MLC2V, and SNX13 genes plus two genes (AK1, PPIA) used as housekeeping for muscle tissue were assigned to porcine chromosomes using the INRA-Minnesota 7000 rads radiation hybrid panel (IMpRH). Our data confirm and refine the cytogenetic position of the KALRN, AK1, PPIA genes, improve the existing physical map of MYH1 and assign two new genes (MLC2V and SNX13) to swine chromosomes.